Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Post-doctoral Fellowship in longitudinal image analysis at UCL
by Arman Eshaghi 14 Oct '15

14 Oct '15

Apologies for the spam, we thought this might be of interest for Freesurfer users. A postdoctoral position in longitudinal image analysis is available within the Centre for Medical Image Computing (CMIC) at UCL Department of Computer Sciences, London, UK. We are seeking a highly motivated individual to work within the Progression of Neurological Disease (POND) Group cmic.cs.ucl.ac.uk/pond, led by Prof. Daniel Alexander, on computational-statistical neurological disease progression within the Horizon 2020 EuroPOND project: www.europond.eu. See http://cmic.cs.ucl.ac.uk/pond/vacancies/ for more details and the application procedure. If you have any queries regarding the vacancy or the application process please contact Dr Neil Oxtoby n.oxtoby(a)ucl.ac.uk. ————————————————————————— Arman Eshaghi, MD PhD Student UCL Institute of Neurology Queen Square Multiple Sclerosis Centre 1st Floor, Russell Square House 10-12 Russell Square London WC1B 5EH Tel: (+44) (0) 203 108 7420 UCL extension: 57420 arman.eshaghi.14(a)ucl.ac.uk Website: http://www.homepages.ucl.ac.uk/~skgtaes/

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Problem with recon-all
by Mads Jensen 13 Oct '15

13 Oct '15

Hi, I got a problem with recon-all of T1's. The problem is that the surfaces extent into what is essential noise, see linked images. The problem is reoccurring in all the subjects I have ran so far, so I was wondering if there could be a generic fix or if it will be necessary to fix each recon individually. The sequence is a MP2RAGE recorded from a Siemens Skyra. thanks, mads https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0005_sagittal.j… https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0006_sagittal.j… https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_coronal.jpg https://dl.dropboxusercontent.com/u/915037/recon_marked/sub_0007_sagittal.j…

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Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache
by Martin Reuter 13 Oct '15

13 Oct '15

Hi Bhavani, when I run mris_label_calc intersect MPS-007_2mod.long.MPS-007\ rh.cortex.label MPS-\ 007\ lh.cortex.label out.label it goes through and writes the out.label file. I used fs 5.3 for that. Can you please send me the command and input files that fail for you? About your other questions: qdec tables should be stored in <SUBJECS_DIR>/qdec not sure about the other error. can you send the cross qdec table. probably you need a level file for group? Thanks, Martin P.S. Please post questions to the FreeSurfer list. On 10/13/2015 10:56 AM, Selvaraj, Bhavani wrote: > Hi Martin, > Thanks for the reply. Yes those files are available at these locations. > when I run this command for LH > long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR > it runs smoothly > and gave me these results > tksurfer MPS-007 lh pial -overlay /Applications/freesurfer/subjects/MPS-007/surf/lh.long.thickness-avg.fwhm25.mgh > tksurfer MPS-005 lh pial -overlay /Applications/freesurfer/subjects/MPS-005/surf/lh.long.thickness-avg.fwhm25.mgh > > but for the rh only the patients MPS-007 gave me the error MPS-005 worked fine. > How do I fix that? > I am attaching you the cortex label file I don't know how to tell if it is corrupted. > > Also I have two more question where should I store the QDEC data table > Is this where I should make it? > Applications/freesurfer/subjects/qdec/ long.qdec.table.dat > > also when I try to open the table in Qdec I get the following error: > freesurfer% qdec --table ./qdec/cross.qdec.table.dat > > Reading /Applications/freesurfer/tktools/tkUtils.tcl > > Using /Applications/freesurfer/lib/tcl/fsgdfPlot.tcl > > Loading data table ./qdec/cross.qdec.table.dat... > Number of columns: 13 > fsid column: 1 > Number of factors: 12 > Number of subjects: 2 > ERROR: QdecSubject::GetContinuousFactor failure: could not find factor name: Group for subject MPS-007 > > Thanks Martin for your help! > bhavani > > > ________________________________________ > From: Martin Reuter [mreuter(a)nmr.mgh.harvard.edu] > Sent: Friday, October 09, 2015 8:59 PM > To: Selvaraj, Bhavani > Subject: Re: [Freesurfer] mris__label__calc intersect error in longitudinal qcache > > Hi Bhavani, > > Strange, are those files available at those locations? Can you also check permissions. Open the label files to see if they are corrupted. > Best MartinOn Oct 9, 2015 11:31 AM, "Selvaraj, Bhavani" <Bhavani.Selvaraj(a)nationwidechildrens.org> wrote: >> Hi, >> >> when I try running longitudinal analysis for 2 subjects I get the following error (this error >> >> only persists for the right hemisphere-- left hemisphere works fine for this subject). >> >> >> >> mris_label_calc intersect /Applications/freesurfer/subjects/MPS-007_2mod.long.MPS-007/label/rh.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label /Applications/freesurfer/subjects/MPS-007/label/rh.long.cortex.label >> >> >> >> ERROR -11 : mris_label_calc intersect did not work? >> >> I saw a similar question in the archived mail list so I tried running this command by itself and this was the comment >> >> Segmentation fault >> >> I didn’t know how to fix this error? should I run them again?? >> >> >> >> >> >> Qdec table >> >> Fsid fsid-base years >> >> MPS-007_1 MPS-007 3 >> >> MPS-007_2mod MPS-007 4 >> >> MPS-007_3 MPS-007 4 >> >> MPS-005_1 MPS-005 5 >> >> MPS-005_2 MPS-005 6 >> >> MPS-005_3 MPS-005 6 >> >> >> >> >> >> Thanks, >> >> Bhavani > > 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 > https://urldefense.proofpoint.com/v2/url?u=http-3A__www.partners.org_compli… . 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. -- 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

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FSL GUI error message
by Park, Jung Mi 13 Oct '15

13 Oct '15

Hello When I ran FSL GUI on the Martinos center after typing source freesurfer, I received an error message like that custom widget with id loop-button does not return a valid node on the X-window terminal. How can I solve this problem? Thanks Jung Mi I used FSL 5.0.7, FEAT tool v 6.00 for FSL GUI through the brain vision at Martinos center. Next the information I set: feat main script: /bin/cp /tmp/feat_9l88ef.fsf design.fsf /usr/pubsw/packages/fsl/current/bin/feat_model design mkdir .files;cp /usr/pubsw/packages/fsl/current/doc/fsl.css .files;ln -s /usr/pubsw/packages/fsl/current/doc/images .files/images /usr/pubsw/packages/fsl/current/bin/fsl_sub -T 10 -l logs -N feat0_init /usr/pubsw/packages/fsl/current/bin/feat /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/design.fsf -D /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat -I 1 -init 19094 /usr/pubsw/packages/fsl/current/bin/fsl_sub -T 78 -l logs -N feat2_pre -j 19094 /usr/pubsw/packages/fsl/current/bin/feat /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/design.fsf -D /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat -I 1 -prestats Preprocessing:Stage 1 /usr/pubsw/packages/fsl/current/bin/mainfeatreg -F 6.00 -d /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+++++.feat -l /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/logs/feat2_pre -R /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/report_unwarp.html -r /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/report_reg.html -i /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/FEAT7+.feat/example_func.nii.gz -n 10 -h /autofs/cluster/catanagp/users/jumi/subjects/functional/sess07/bold/006/maaike/fsl_T1 -w 3 -x 90 -s /autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/5.0.7/data/standard/MNI152_T1_2mm_brain -y 12 -z 90 Option -s ( standard image ) selected with argument "/autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/5.0.7/data/standard/MNI152_T1_2mm_brain"

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Re: [Freesurfer] error in atlas creation
by Anthony Dick 13 Oct '15

13 Oct '15

Hello Bruce, We have tried running the atlas creation on newly freesurfed brains with the latest FS version and keep getting the same error. We have essentially replicated the error we get on our own manually edited volumes by copying the aparc+aseg.mgz and renaming it seg_edited.mgz. Thus, it is unlikely to be a problem with our manually edited brains. This results in the following error at the same place (running the rebuild_gca_atlas.csh script): == Number of threads available to mri_em_register for OpenMP = 16 == reading 23 input volumes... logging results to talairach_one.log reading '<path>/average/RB_one_2015-10-13.gca'... average std = 9.8 using min determinant for regularization = 9.7 0 singular and 426 ill-conditioned covariance matrices regularized reading '<path>/009/mri/nu.mgz'... reading '<path>/average/RB_one_2015-10-13.gca'... reading frame -1 of gca INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() INFO: MRImask() using MRImaskDifferentGeometry() reading '<path>/009/mri/transforms/talairach_one.lta'... mri_read(): couldn't determine type of file <path>/009/mri/transforms/talairach_one.lta mri_em_register: could not open input volume <path>/009/mri/transforms/talairach_one.lta. Perhaps the FS folks could try to replicate this error? You don't need my brains, just a couple of FS'd brains with a file called seg_edited.mgz. If you don't get the error, then maybe it is a problem with our local settings (although we get this error on multiple different computers). Thanks for any help! Anthony On 7/20/15 2:30 PM, Anthony Dick wrote: > Hello, > > I was wondering if these got uploaded correctly. Please let me know if > I made a mistake and thanks, > > Anthony > > On 7/9/15 1:41 PM, Bruce Fischl wrote: >> sure >> On Thu, 9 Jul 2015, Anthony Dick wrote: >> >>> Hello Bruce, >>> >>> I am still getting this error after re-running autorecon1 in the newest >>> version of FS. Can I upload two brains and see what is the issue? I'm a >>> bit stumped on this one. >>> >>> Anthony >>> >>> On 5/26/15 12:21 PM, Bruce Fischl wrote: >>>> Hi Anthony >>>> >>>> sorry, I know you've posted this before. What version are you running? >>>> And what type is your labeled data? That is, are they uchar? int? >>>> At some >>>> point this used to not work with non-uchar data, but I think I >>>> fixed it a >>>> while ago. YOu might try downloading a beta of V6 and see if it >>>> fixes your >>>> problem >>>> >>>> cheers >>>> Bruce >>>> >>>> >>>> On Tue, 26 >>>> May 2015, Anthony Dick wrote: >>>> >>>>> Hello, >>>>> >>>>> I have been stumped by this error I keep getting using the >>>>> rebuild_gca_atlas.csh script. I am trying to build a cerebellar >>>>> atlas, >>>>> so I am wondering if the problem is with the brains we >>>>> parcellated, or >>>>> with my installation etc. The brains consist of manually segmented >>>>> cerebellums from the original T1. The T1 is run through >>>>> Freesurfer, and >>>>> the ROIs are made in Freeview. The edited file is called >>>>> seg_edited.mgz. >>>>> Things run smoothly up until this error: >>>>> >>>>> using MR volume /<path>/subjects/4/mri/brain.mgz to mask input >>>>> volume... >>>>> reading 23 input volumes... >>>>> logging results to talairach_one.log >>>>> reading 'subjects/average/RB_one_2015-05-14.gca'... >>>>> gcaAllocMax: node dims 32 32 32 >>>>> gcaAllocMax: prior dims 128 128 128 >>>>> gcaAllocMax: max_labels 0 >>>>> average std = 8.4 using min determinant for regularization = 7.1 >>>>> 0 singular and 119 ill-conditioned covariance matrices regularized >>>>> reading '/<path>/subjects/4/mri/nu.mgz'... >>>>> reading '/<path>/subjects/average/RB_one_2015-05-14.gca'... >>>>> gcaAllocMax: node dims 32 32 32 >>>>> gcaAllocMax: prior dims 128 128 128 >>>>> gcaAllocMax: max_labels 0 >>>>> reading frame -1 of gca >>>>> MRIcopyFrame: src and dst must be same type >>>>> reading '/<path>/subjects/4/mri/transforms/talairach_one.lta'... >>>>> mri_read(): couldn't determine type of file >>>>> /<path>/subjects/4/mri/transforms/talairach_one.lta >>>>> mri_em_register: could not open input volume >>>>> /<path>/subjects/4/mri/transforms/talairach_one.lta. >>>>> >>>>> >>>> _______________________________________________ >>>> 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 > -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: adick(a)fiu.edu Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu Join the Society for the Study of Human Development: http://www.sshdonline.org

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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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