Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

how to obtain subjects cortical thickness and then analyze unpair t-test
by Rujing Zha 19 Nov '13

19 Nov '13

Dear all, Ater recon-all,which image can I select to group t-test? And do they need process in advance? Thanks very much. All the best. 2013-11-19 Rujing Zha

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Fwd: RLE Lossless dicom compression
by Nathaniel Reynolds 19 Nov '13

19 Nov '13

Hi, I'm working with some clinical DICOMs which appear to have their image data compressed with a RLE lossless algorithm. I need to decompress these images. When I run into jpeg compression, I can use the "dcmdjpeg" function. The "dcmdjpeg" function doesn't work on the RLE-compressed files, naturally. I can't find an equivalent function for RLE-lossless decompression. Does anybody know of one? Thanks, Nathaniel

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lobe mapping
by Mojdeh Zamyadi 19 Nov '13

19 Nov '13

Hi all, I'm interested in getting a lobar segmentation of the cortex and I've already ran recon-all on my subjects. I'm now confused by the outputs and was wondering if someone could tell me which output file contains segmentation that can be merged to get a 4 lobe parcellation similar to: http://freesurfer.net/fswiki/CorticalParcellation? Thanks a lot, -Mojdeh

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Recon-all problem
by Devin Sodums 19 Nov '13

19 Nov '13

Dear Freesurfer experts, I have recently installed Freesurfer onto a VirtualBox Linux environment, and had no problems running the supplied practice subject, 'Bert', all the way through reconstruction. However, when I started trying to analyze my own subject's, recon-all keeps exiting just after the "mri_nu_correct.mni" step, without any specific error message. I have copied and pasted the error message from the unsuccessful, and successful run below, as well as the output from the "bugr" command. I realize that tcsh is out of date, and I have tried updating it (which I am not sure if I was successful or not), but I got the same message with the successful run so I don't think that is the issue. Any suggestions would be greatly appreciated. Best, Devin General info: fsuser@xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/b_s_20131018_124417$ which freesurfer /usr/local/freesurfer/bin/freesurfer FREESURFER_HOME: /usr/local/freesurfer Build stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Debian version: wheezy/sid Kernel info: Linux 3.2.0-56-generic i686 Unsuccessful Run: xubuntu-VirtualBox:~/share/SMIP_MNI_structural_files/boucher_suzanne_20131018_12 4417> recon-all -subjid b_s_20131018_fs -all WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417 Actual FREESURFER_HOME /usr/local/freesurfer Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux #-------------------------------------------- #@# MotionCor Fri Nov 15 16:30:12 EST 2013 Found 1 runs /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig/001.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs mri_convert /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz --conform mri_convert /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz --conform $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.0156845, -0.970744, 0.239606) j_ras = (0.0185749, 0.239877, 0.970626) k_ras = (0.999704, 0.0107731, -0.0217938) Original Data has (1, 1, 1) mm size and (256, 256, 176) voxels. Data is conformed to 1 mm size and 256 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz... mri_add_xform_to_header -c /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/transforms/talairach.xfm /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri/orig.mgz INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Nov 15 16:30:45 EST 2013 /home/fsuser/share/SMIP_MNI_structural_files/b_s_20131018_124417/b_s_20131018_fs/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s b_s_20131018_fs exited with ERRORS at Fri Nov 15 16:30:58 EST 2013 SUCCESSFUL RUN: INFO: extension is mgz #-------------------------------------------- #@# Talairach Fri Nov 15 15:53:35 EST 2013 /usr/local/freesurfer/subjects/bert/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Fri Nov 15 15:55:03 EST 2013 /usr/local/freesurfer/subjects/bert/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm talairach_afd: Talairach Transform: transforms/talairach.xfm OK (p=0.7614, pval=0.6675 >= threshold=0.0050) awk -f /usr/local/freesurfer/bin/extract_talairach_avi_QA.awk /usr/local/freesurfer/subjects/bert/mri/transforms/talairach_avi.log tal_QC_AZS /usr/local/freesurfer/subjects/bert/mri/transforms/talairach_avi.log TalAviQA: 0.97409 z-score: 0 #-------------------------------------------- #@# Nu Intensity Correction Fri Nov 15 15:55:03 EST 2013 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 /usr/local/freesurfer/subjects/bert/mri /usr/local/freesurfer/bin/mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 nIters 2 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Linux xubuntu-VirtualBox 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 17:31:43 UTC 2013 i686 i686 i386 GNU/Linux Fri Nov 15 15:55:03 EST 2013 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on 2010-02-20 at 20:19:13 tmpdir is ./tmp.mri_nu_correct.mni.10351 /usr/local/freesurfer/subjects/bert/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10351/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.10351/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.10351/nu0.mnc...

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Re: [Freesurfer] Aseg2feat: Missing segmentations
by Douglas N Greve 19 Nov '13

19 Nov '13

Can you send the aseg2feat log file? Also, please remember to post to the list instead of to me personally. thanks! doug On 11/19/2013 03:17 PM, Sudhin A. Shah wrote: > yes, it looks fine.. > ________________________________________ > From: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > Sent: Tuesday, November 19, 2013 2:50 PM > To: Sudhin A. Shah; Freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Aseg2feat: Missing segmentations > > Those are some big segs. Have you checked the registration? > > > On 11/19/2013 02:41 PM, Sudhin A. Shah wrote: >> yes :) For example in this 1 subject segs ( >> 2005 2008 2010 2011 2013 2021 2023 2025 2029 1005 1008 1011 1013 1021) are all missing.. >> >> The missing segs are not consistent across subjs(i.e. other subjs have different segs missing). I chose a list of 86 segs to 'cover' the brain and not sure if I was over-reaching..Also some segs are reading with value 100 (i.e. all voxels have a value of 100)? >> >> >> >> ________________________________________ >> 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: Tuesday, November 19, 2013 2:34 PM >> To: freesurfer(a)nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Aseg2feat: Missing segmentations >> >> there were probably some small segmentations that were lost. Is this >> causing a problem? >> On 11/19/2013 02:22 PM, Sudhin A. Shah wrote: >>> Hello, >>> >>> This is regarding the registration of functional data to freesurfer >>> parcellations >>> (http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace) >>> >>> The rsfMRI is sampled at 2x2x2. >>> >>> After running reg-feat2anat and aseg2feat >>> >>>>> a = MRIread('aparc+aseg'); %Original aparc+aseg output from >>> freesurfer recon-all >>>>> size(unique(a.vol(:))) % 114 segs >>>>> a = MRIread('aparc+aseg'); % this is the output file after aseg2feat >>>>> size(unique(a.vol(:))) % 98 segs >>> Any advice? >>> >>> Thanks >>> >>> >>> >>> _______________________________________________ >>> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > -- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Aseg2feat: Missing segmentations
by Douglas N Greve 19 Nov '13

19 Nov '13

Those are some big segs. Have you checked the registration? On 11/19/2013 02:41 PM, Sudhin A. Shah wrote: > yes :) For example in this 1 subject segs ( > 2005 2008 2010 2011 2013 2021 2023 2025 2029 1005 1008 1011 1013 1021) are all missing.. > > The missing segs are not consistent across subjs(i.e. other subjs have different segs missing). I chose a list of 86 segs to 'cover' the brain and not sure if I was over-reaching..Also some segs are reading with value 100 (i.e. all voxels have a value of 100)? > > > > ________________________________________ > 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: Tuesday, November 19, 2013 2:34 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Aseg2feat: Missing segmentations > > there were probably some small segmentations that were lost. Is this > causing a problem? > On 11/19/2013 02:22 PM, Sudhin A. Shah wrote: >> Hello, >> >> This is regarding the registration of functional data to freesurfer >> parcellations >> (http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace) >> >> The rsfMRI is sampled at 2x2x2. >> >> After running reg-feat2anat and aseg2feat >> >>>> a = MRIread('aparc+aseg'); %Original aparc+aseg output from >> freesurfer recon-all >>>> size(unique(a.vol(:))) % 114 segs >>>> a = MRIread('aparc+aseg'); % this is the output file after aseg2feat >>>> size(unique(a.vol(:))) % 98 segs >> Any advice? >> >> Thanks >> >> >> >> _______________________________________________ >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Aseg2feat: Missing segmentations
by Sudhin A. Shah 19 Nov '13

19 Nov '13

Hello, This is regarding the registration of functional data to freesurfer parcellations (http://freesurfer.net/fswiki/FsTutorial/MapSegmentationsToFunctionalSpace) The rsfMRI is sampled at 2x2x2. After running reg-feat2anat and aseg2feat >> a = MRIread('aparc+aseg'); %Original aparc+aseg output from freesurfer recon-all >> size(unique(a.vol(:))) % 114 segs >> a = MRIread('aparc+aseg'); % this is the output file after aseg2feat >> size(unique(a.vol(:))) % 98 segs Any advice? Thanks

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Re: [Freesurfer] localGI Matlabpath
by Marie Schaer 19 Nov '13

19 Nov '13

Christiane, The log you sent me doesn't correspond to the error you first wrote in your email. The error reads as follow in your log: --------------- >> reading filled volume... closing volume... {??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); } >> ERROR: make_outer_surface did not create output file '/data/Projekte/Freesurfer/Prob1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux beo-08 2.6.32.59-ql-beowulf-37 #1 SMP Sat Mar 31 14:31:51 CEST 2012 x86_64 GNU/Linux recon-all -s Prob1 exited with ERRORS at Tue Nov 19 08:02:22 CET 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting --------------- It doesn't find the fspecial.m function, probably because you don't have the licence for the image processing toolbox in your installation. Is there a way you can add the toolbox to your matlab installation? Marie NB: no need to change the matlab path, it's already correctly set up On Nov 18, 2013, at 11:26 PM, "Jockwitz, Christiane" <c.jockwitz(a)fz-juelich.de<mailto:c.jockwitz@fz-juelich.de>> wrote: Hi Marie, with the old path I ment that the path just did not change. Here is my entire log. Thank you very much for your help. Kind regards Christiane Von: Marie Schaer [mailto:Marie.Schaer@unige.ch<http://unige.ch>] Gesendet: Montag, 18. November 2013 21:03 An: Jockwitz, Christiane Cc: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Betreff: Re: [Freesurfer] localGI Matlabpath Hi Christiane, What do you mean when you say that you get the old path with getmatlab? In any case, the error seems not related to a matlab path issue. Can you please attach the entire log? Marie On Nov 18, 2013, at 12:03 AM, "Jockwitz, Christiane" <c.jockwitz(a)fz-juelich.de<mailto:c.jockwitz@fz-juelich.de>> wrote: Dear Freesurfer experts, I tried to run the local GI command recon-all –s –localGI and got the following error message: >> ??? Undefined function or method 'make_outer_surface' for input arguments of type 'char'. >From earlier post I tried to fix the problem by changing the matlabpath like this: setenv MATLABPATH /directory/bin > setenv PATH ${MATLABPATH}/bin:${PATH} However, if I then check the path via „getmatlab“ I still get the old path. Did I do something wrong? And is it right to set up my matlabpath to the matlab/bin folder? The scripts like make_outer_surface.m are located in the freesurfer/matlab directory. Or does the path have to point to the scripts directly? Thank you very much in advance Kind regards, Christiane ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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. <recon-all.log>

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Neuroimaging Research Technician II Position at VA Boston
by Benjamin Trotter 19 Nov '13

19 Nov '13

*Neuroimaging Research Technician--II* A Neuroimaging Research Technician position is available in the VA Boston Healthcare System (VABHS) Neuroimaging Research for Veterans (NeRVe) Center (Director: Dr. David Salat). Applicants must be a U.S. citizen. The Neuroimaging Research Technician will provide technical support for image preprocessing and analysis (using programs such as FSL and FreeSurfer), maintenance and development of in-house custom processing codes (script writing in unix/linux, matlab, etc), and assist staff members in the conduct of neuroimaging research as well as administrative tasks related to the Center. This includes developing expertise and training other investigators with the operation of current MRI hardware (scanner console, goggles, headphones, BioPac system, etc) and software for data processing and analysis. Additional responsibilities will include management of online documentation and center resources. Technical skills and familiarity with Linix/Unix, Matlab, and imaging software packages such as FSL and FreeSurfer is beneficial. Applicants should have a minimum of a Bachelor’s degree, with a background in Neuroscience, Computer Science, Engineering, Math or Physics. A two year commitment is required. Interested candidates should email a cover letter, resume, and contact information for two professional references to Dr. Meghan Robinson at meghan.robinson(a)va.gov.

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longitudinal 5.3 used with baseline fs 5.1 recon-all
by Knut J Bjuland 19 Nov '13

19 Nov '13

Hi,we have finished cross sectional scanworkups in Freesurfer 5.1 and gone through qa. Can we use these scanworkups for further processing in the longitudinal stream in Freesurfer 5.3? Knut J

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Freesurfer November 2013