Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 discussions

Freesurfer from source library dependencies dead link
by King, Maximilian 22 Dec '18

22 Dec '18

External Email - Use Caution Hi Freesurfer folks! I am attempting to build freesurfer from source for our HPC center here at Brown University, but are running into a snag. Looks like the documentation points to a dead link for Step 3 of the freesurfer_linux_developers_page <https://surfer.nmr.mgh.harvard.edu/fswiki/freesurfer_linux_developers_page> where we are required to get the prebuilt bundle of 3rd party dependancies using: wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x… However, the command fails as the directory does not exist. $ wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x… --2018-12-21 11:07:49-- ftp://surfer.nmr.mgh.harvard.edu/pub/dist/fs_supportlibs/prebuilt/centos6_x… => ‘centos6-x86_64-packages.tar.gz’ Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu) 132.183.240.105 Connecting to surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)|132.183.240.105|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD (1) /pub/dist/fs_supportlibs/prebuilt/centos6_x86_64 ... No such directory ‘pub/dist/fs_supportlibs/prebuilt/centos6_x86_64’. Any chance I could get the updated path for these dependencies? Happy holidays! Cheers, Max -- *Maximilian King, MSc* HPC Application Scientist Center for Computation and Visualization Brown University Computing and Information Systems 180 George St, Providence, RI 02906, USA Tel: +1 (401) 863-7448 *maximilian_king(a)brown.edu* <maximilian_king(a)brown.edu> *http://ccv.brown.edu* <http://ccv.brown.edu/>

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Error while saving NPC results
by Daniel Leopold 21 Dec '18

21 Dec '18

External Email - Use Caution Dear Drs. Winkler, Greve, Fischl, et al. Could you help me understand which palm options are needed in order to produce tfce and clustere NPC results that are fwe-corrected across contrasts (i.e., _cfwep_)? I'm analyzing area and thickness and have four one-tailed contrasts of interest (e.g., C1+, C1-, C2+, C2-). Currently, I am only able to get the "output'_dpv_npc_fisher_cfwep_c[1234]" results, but the palm log ends abruptly after saving these files and does not save the _tfce_ or _clustere_ versions: Saving p-values for NPC between modalities (uncorrected and corrected within contrasts). Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c1 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c1 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c1 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c1 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c1 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c2 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c2 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c2 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c2 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c2 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c3 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c3 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c3 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c3 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c3 Saving file: wordadhd_npc_lh_dpv_npc_fisher_fwep_c4 Saving file: wordadhd_npc_lh_clustere_npc_fisher_c4 Saving file: wordadhd_npc_lh_clustere_npc_fisher_fwep_c4 Saving file: wordadhd_npc_lh_tfce_npc_fisher_c4 Saving file: wordadhd_npc_lh_tfce_npc_fisher_fwep_c4 Saving p-values for NPC between modalities (corrected across contrasts). Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c1 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c2 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c3 Saving file: wordadhd_npc_lh_dpv_npc_fisher_cfwep_c4 >> The error log contains the following text, and my efforts to read through these source files have been in vain: {^HCell contents reference from a non-cell array object. Error in palm_saveall (line 1043) distmax(:,j) = plm.Tclumax{m}{c}; Error in palm_core (line 2489) palm_saveall(plm,opts); Error in palm (line 81) palm_core(varargin{:}); }^H ^G I have essentially permuted the various -corr(con/mod) and -npc(con/mod) options, as well as various combinations of -T & -C {z}, -Tuni & -Cuni {z}, and -Tnpc & -Cnpc {z}, using a small number of permutations to assess the number of output maps and whether jobs finish appropriately. Here's an example of one of the palm commands that resulted in these output and error logs (with line-breaks for legibility): fsl_sub -l $logdir palm -designperinput -i {area_dir}/292_${hemi}.area_stack.mgh -d {design_dir}/wordadhd_npc_areatotal.mat -t {design_dir}/wordadhd_npc_areatotal.con -i {thickness_dir}/292_${hemi}.thickness_stack.mgh -d {design_dir}/wordadhd_npc_thickmean.mat -t {design_dir}/wordadhd_npc_thickmean.con -m {base_dir}/palm/input/${hemi}mask.mgz -s ${surf_dir}/${hemi}.white ${surf_dir}/${hemi}.white.avg.area.mgh -o wordadhd_npc_${hemi} -eb ${EB} -corrcon -corrmod -logp -ise -npc -T -C 1.64485 -n 5 If knowing versions helps at all: PALM alpha109 MATLAB 8.3.0.532 (R2014a) FreeSurfer 5.3.0 FSL 5.0.8 Any advice you could provide on this particular error, why my input doesn't produce the tfce_cfwep or clustere_cfwep results, or other problem-solving suggestions would be greatly appreciated! With gratitude, Dan

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mris_fwhm problem
by shahin＠nmr.mgh.harvard.edu 21 Dec '18

21 Dec '18

Dear Surfers, I am trying to use mris_fwhm to apply fwhm=0.66 to my fmri data (voxel size 1 mm iso)using the below command: mris_fwhm --s <SBJ_NAME>--hemi rh --smooth-only --i fmcpr.sm0.self.projfrac_0.rh.nii.gz --fwhm 0.66 --o fmcpr.sm0p66_surf.self.projfrac_0.rh.nii.gz --mask /masks/brain.self.rh.nii.gz When I apply this command, it works without any error. The message on screen is as below: <SBJ_NAME> rh white Number of vertices 160391 Number of faces 320778 Total area 102725.085938 GroupSurface 0 AvgVtxArea 0.640467 AvgVtxDist 0.875515 StdVtxDist 0.253406 Loading mask masks/brain.self.rh.nii.gz Found 36045 voxels in mask Not Polynomial detrending Smoothing input by fwhm=0.660000, gstd=0.280276, niters=0 Only smoothing, so saving and exiting now But the outcome is the same as input. I think it is expected based on (niters=0). When I use the same command with fwhm =1, then i see the difference and niters=1. My question is, why is fwhm = 0.66 not acceptable? How can i solve this issue. Regards _____________________________________ Shahin Nasr Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129

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Re: [Freesurfer] surfreg cannot allocate memory
by fsbuild 21 Dec '18

21 Dec '18

External Email - Use Caution Hello Haoran, You could try looking at your shell limits and see if the memory size is listed as something other than “unlimited”.   In bash shell, $ bash $ ulimit -a core file size          (blocks, -c) 0 data seg size           (kbytes, -d) unlimited scheduling priority             (-e) 0 file size               (blocks, -f) unlimited pending signals                 (-i) 256605 max locked memory       (kbytes, -l) 64 max memory size         (kbytes, -m) unlimited open files                      (-n) 65535 pipe size            (512 bytes, -p) 8 POSIX message queues     (bytes, -q) 819200 real-time priority              (-r) 0 stack size              (kbytes, -s) unlimited cpu time               (seconds, -t) unlimited max user processes              (-u) 256605 virtual memory          (kbytes, -v) unlimited file locks                      (-x) unlimited If memory does not read as unlimited then, $ ulimit -m unlimited - R. On Dec 19, 2018, at 18:30, Haoran Xu <haoran.x(a)gmail.com> wrote:        External Email - Use Caution        Hello FreeSurfer Developers,I am using surfreg to map one of my subject "subj001" to "fsaverage_sym" by these commands:surfreg --s subj001 --t fsaverage_sym --lhsurfreg --s subj001 --t fsaverage_sym --lh --xhemiThe first command worked well, however the second did not. It showed error:"znzTAGskip: tag=1952870258, failed to calloc 1768846336 bytes!Cannot allocate memory"Searched the archive but without good luck. Any suggestions? Appreciated!1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. 2) Platform: UBUNTU 16.04 LTS with 23.5GB memory and 1.4TB available space. (With this, 1.7G should be fine.)3) uname -a: Linux haoranPC 4.15.0-43-generic #46~16.04.1-Ubuntu SMP Fri Dec 7 13:31:08 UTC 2018 x86_64 x86_64 x86_64 GNU/LinuxRegards, Haoran Xu_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Postdoctoral position at UCL
by Arman Eshaghi 21 Dec '18

21 Dec '18

External Email - Use Caution Apologies for the cross-posting and wide distribution. Postdoc advertisement ================== The NMR Research Unit is a multidisciplinary research team focusing on multiple sclerosis (MS). A Research Fellow is sought to work primarily on the development and optimisation of a high-dimensional model to predict individual treatment responses in MS, as part of an NIHR Research Professorship awarded to Professor Olga Ciccarelli. This is a collaborative project with Dr Parashkev Nachev's team, who are working on the creation of individually predictive models of clinical outcome from high-dimensional analysis of large-scale clinical datasets The project aims to create a prototype software that predicts whether an individual patient with MS will respond to a medication by using machine learning techniques (a crucial step towards "personalized medicine"). All the elements constituting an individual MS profile will be collected prospectively in a large-scale registry. The post holder will be responsible for organising the project database on XNAT, developing probabilistic, high-dimensional models that can achieve high individual predictive value, assisting with the day-to-day running of the project, and co-ordinating public and patient engagement (PPE) and involvment (PPI) activities. The post is available immediately and is funded by a grant from the NIHR for three years in the first instance. Apply here: https://atsv7.wcn.co.uk/search_engine/jobs.cgi?SID=amNvZGU9MTc4NDY5OSZ2dF90… You can get in touch with me (a.eshaghi(a)ucl.ac.uk) for more information. Best wishes, Arman Eshaghi, MD, PhD Research Associate Queen Square Multiple Sclerosis Center Queen Square UCL Institute of Neurology University College London United Kingdom

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mris preproc for folding index
by Martin Juneja 20 Dec '18

20 Dec '18

External Email - Use Caution Hi, Just like volume, I have "Folding Index" measures saved in lh/rh.aparc.stats files for each subject. If I am using mris_preproc *--meas volume* --out CV/lh.CV.mgh command to concat cortical volume files from all subjects, then how can I use this command for "folding index" output file? Any help will be really appreciated.

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using custom surface template
by Jason Tourville 20 Dec '18

20 Dec '18

External Email - Use Caution Hello FreeSurfers, We use a custom surface template, generated according to the instructions in the SurfaceRegAndTemplates <https://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates> instructions for inter-subject co-registration. We then do cortical labeling and extract surface and volume stats. In the past, I would re-run mris_register, then jump to labeling using the resulting ?h.sphere.reg (using either a custom atlas or the labeled template surface), and then extract stats. However, I now see that there are steps in -autorecon3 stage of the recon-all workflow, including the pial surface generation step, that are done after the -surfreg step, but prior to stat extraction, that depend on ?h.sphere.reg. So it seems like I should be running the essentially the entire -autorecon3 stage (minus -sphere and the default surface labeling and stat extraction steps) with the custom surface template as input. Is that the case? If so, is there an "expert flag" to run these steps of -autorecon3 with a custom surface template (analogous to the -custom-tal-atlas flag for early stages?) Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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x y dimension mismatch dt_recon
by Renew Andrade 20 Dec '18

20 Dec '18

External Email - Use Caution Dear community: I have an issue that I have seen in the past still don´t know how to fix. Bval shows rows of 16 values and bvecs 17 values in one row only the rest 2 show 16 as apparently should be. What can I do? Sincerely, Andrade.

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subject IDs for qdec
by Helen Beaumont 20 Dec '18

20 Dec '18

External Email - Use Caution Please, what format should the subject IDs have for qdec. At the moment my subjects IDs are alphanumeric (e.g. h00013), and although the SUBJECTS_DIR is set correctly, the files are not being found. I have changed the first to numeric only (024), but it is also not found. I attach the .dat file, and below is the error when I try to load the table: Data table /media/QuantimaPoP/Humans_AllProcessed/FS_for_qcache/qdec/qdec.table.dat loaded. SUBJECTS_DIR is '/media/QuantimaPoP/Humans_AllProcessed/FS_for_qcache' Verifying subject data.sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject '024' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'h00025' in SUBJECTS_DIR .sh: 1: Syntax error: Bad fd number Thanks for any help Helen Beaumont PhD Manchester NeuroImaging

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Re: [Freesurfer] FreeSurfer: trouble processing subjects
by Diamond, Bram Ryder 20 Dec '18

20 Dec '18

Hi Andrade, I'm adding the FreeSurfer support list so other can benefit. To answer your question, you would use the first dicom from the diffusion scan... but since you don't have the dicoms that won't work. You can combine all of the DTI nifty files into one multi-frame diffusion 4d volume using mri_concat. mri_concat /path/to/all/IXI025-Guys-0852-DTI-??.nii.gz --o /output/path/dti.mgz Then run dt_recon using dti.mgz as your input. cd /path/to/desired/subjects/dir export SUBJECTS_DIR=$(pwd) dt_recon --b /path/to/bvals.txt /path/to/bvecs.txt--i /path/to/dti.mgz --s andrade --o /path/to/desired/diffusion/output Let me know if this works. Best, Bram Bram R. Diamond, BSc Research Technician II Laboratory for Computational Neuroimaging Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street Charlestown, MA 02129 (p): 617-726-6598 ________________________________________ From: Renew Andrade <andraderenew(a)yahoo.com> Sent: Thursday, December 20, 2018 10:12:31 AM To: Diamond, Bram Ryder Subject: Re: FreeSurfer: trouble processing subjects External Email - Use Caution I don'tknow if I understand right. I don't have a dicom format file for dtrecons. What I have is nii.gz all that I gave you. In case I need to do dcmunpack either way I need to do dtrecons for each of those dcmunpack or just the first one? Sent from my iPhone > On 20 Dec 2018, at 15:46, Diamond, Bram Ryder <BRDIAMOND(a)mgh.harvard.edu> wrote: > > Hi Andrade, > > You should be submitting the IXI025-Guys-0852-T1.nii.gz for recon-all. This seems to be working fine with freesurfer v6.0 on my machine. > > cd /path/to/desired/subjects/dir > export SUBJECTS_DIR=$(pwd) > recon-all -i /path/to/IXI025-Guys-0852-T1.nii.gz -s andrade -all > > For the diffusion scan, you will want to run it through dt_recon. If you have the raw dcms, it would easiest to use one of those as input rather than combine all of your directions into one multi-frame volume. You can run unpacksdcmdir to get the first dcm of the diffusion scan. > > cd /path/to/desired/subjects/dir > export SUBJECTS_DIR=$(pwd) > unpacksdcmdir -src /path/to/dicom/dir -targ /path/to/desired/log/output/ -scanonly unpack.log > dt_recon --b /path/to/bvals.txt /path/to/bvecs.txt--i path/to/first/diffusion/dicom.dcm --s andrade --o /path/to/desired/diffusion/output > > I hope this helps. > > Best, > Bram > > Bram R. Diamond, BSc > Research Technician II > Laboratory for Computational Neuroimaging > Martinos Center for Biomedical Imaging > Massachusetts General Hospital > 149 13th Street > Charlestown, MA 02129 > (p): 617-726-6598 > > > ________________________________________ > From: Renew Andrade <andraderenew(a)yahoo.com> > Sent: Wednesday, December 19, 2018 3:13:18 PM > To: Diamond, Bram Ryder > Subject: Re: FreeSurfer: trouble processing subjects > > External Email - Use Caution > > I sent you the whole information but the problem rises in processing with recon-all the DTI files. > > Sent from my iPhone > >> On 19 Dec 2018, at 16:54, Diamond, Bram Ryder <BRDIAMOND(a)mgh.harvard.edu> wrote: >> >> Good morning, Andrade. >> >> I received a message from Bruce that suggests you are having trouble processing a few of your subjects. We received the following file from you via the Martinos Center FileDrop: >> IXI025-Guys-0852-DTI-16.nii.gz >> IXI025-Guys-0852-DTI-14.nii.gz >> IXI025-Guys-0852-DTI-15.nii.gz >> IXI025-Guys-0852-DTI-13.nii.gz >> IXI025-Guys-0852-DTI-12.nii.gz >> IXI025-Guys-0852-DTI-10.nii.gz >> IXI025-Guys-0852-DTI-09.nii.gz >> IXI025-Guys-0852-DTI-11.nii.gz >> IXI025-Guys-0852-DTI-08.nii.gz >> IXI025-Guys-0852-DTI-07.nii.gz >> IXI025-Guys-0852-DTI-05.nii.gz >> IXI025-Guys-0852-DTI-06.nii.gz >> IXI025-Guys-0852-DTI-04.nii.gz >> IXI025-Guys-0852-DTI-03.nii.gz >> IXI025-Guys-0852-DTI-02.nii.gz >> IXI025-Guys-0852-DTI-01.nii.gz >> IXI025-Guys-0852-DTI-00.nii.gz >> bvecs.txt >> bvals.txt >> IXI025-Guys-0852-T1.nii.gz >> >> They seem to be a separated diffusion scan (along with bvec and bcal files), and a T1. In order for me to help you, I need to know what exactly you are having trouble with. >> >> Thanks, >> Bram >> >> >> Bram R. Diamond, BSc >> Research Technician II >> Laboratory for Computational Neuroimaging >> Martinos Center for Biomedical Imaging >> Massachusetts General Hospital >> 149 13th Street >> Charlestown, MA 02129 >> (p): 617-726-6598 >> >> >> >> 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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Freesurfer December 2018