[Freesurfer] motion threshold
Dear FreeSurfers, Due to motion I have to exclude participants from my analysis. Is there an objective measure which could serve as a cut off value concerning motion in the scanner? Can I find it in one of the FreeSurfer files generated through the recon-all process? Subjectively, one can see which images are good or good enough for segmentation. But I'd rather like to include or exclude participants based on an objective threshold. Thank you very much in advance, Best regards, Ines ___ Freesurfer mailing list 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.
[Freesurfer] how to make avgsubject for hippocampal subfields
Dear Freesurfer expert, I'm interested in hippocampal subfields and performed it at each subject. If I'd rather get average hippocampal subfields (volume or surface), what I have to do? The make_average_subject command did not produce it. Does Freesurfer have average hippocampal subfield volume? Best wishes, Jeong -- ___ Freesurfer mailing list 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.
[Freesurfer] Tracula Error: bvecs and bvals don't have the same number of entries
Dear FreeSurfers, I am trying to run trac-all -prep on a single subject, and get the following error: dtifit -k /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dwi.nii.gz -m /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dlabel/diff/aparc+aseg_mask.flt.nii.gz -r /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs -b /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals -o /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/dtifit Error: bvecs and bvals don't have the same number of entries I have searched the message thread, and cannot seem to find a solution applicable to my situation: it seems that the trac-all process generates transposed bvec and bval files. Therefore, I tried transposing these manually and specifying the location to these files (as explained in the tutorial: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), but attempting to run trac-all again still leads to the same result: new bval and bvec files are generated, and I receive the same error message. Does anyone know how I can solve this problem? Thank you, Joy-Loi * My configuration file: setenv SUBJECTS_DIR /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_recons set dtroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data set subjlist = id101 set runlist = 1 set dcmroot = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data set dcmlist = id101/orig/1.dcm set bvalfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvals.txt set bvecfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/id101/dmri/bvecs.txt set nb0 = 10 set doeddy = 1 set dorotbvecs = 1 set thrbet = 0.3 set doregflt = 1 set doregbbr = 0 set doregmni = 1 set mnitemp = /psyklab/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz #set trainfile = /usit/tsd/nevro-work/projects/Memory_project/TRACULA_test/TRACULA_data/subj,train,difftutorial123.txt set pathlist = (lh.cst_AS rh.cst_AS \ lh.ilf_AS rh.ilf_AS \ lh.unc_AS rh.unc_AS \ fmajor_PP fminor_PP \ lh.atr_PP rh.atr_PP \ lh.cab_PP rh.cab_PP \ lh.ccg_PP rh.ccg_PP \ lh.slfp_PP rh.slfp_PP \ lh.slft_PP rh.slft_PP) set ncpts = 5 set usetrunc = 1 * My bvals: 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 700.00 * My bvecs: 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.9998760 0.0011040 0.0157340 -0.7705615 0.6320276 0.0823114 -0.2461791 0.0273479 0.9688392 -0.7953558 0.1076421 0.5965091 0.4620816 -0.8755928 0.1407778 0.2261090 -0.8553081 -0.4661796 0.2601186 0.4095102 -0.8744363 -0.7969547 -0.5877791 0.1392076 -0.5028073 -0.5104712 0.6975709 -0.3073035 0.1334521 -0.9422074 0.7957742 0.1950272 -0.5733304 0.8041493 0.5924478 -0.0484727 -0.1867079 -0.9528833 0.2390659 0.3898569 -0.1063898 0.9147088 0.1341999 -0.6614532 0.7378819 0.3382555 0.8823941 0.3270553 -0.7688307 -0.3139264 -0.5570900 -0.4086013 0.6653325 0.6248017 -0.2933309 0.7581020 -0.5824408 0.7689370 -0.4282441 0.4747016 0.1800972 0.5296402 0.8288835 0.7680658 0.3158178 0.5570763 -0.2214999 0.9744585 0.0370050 -0.4175692 -0.8418782 -0.3418731 -0.1784475 -0.4817282 -0.8579599 0.3361637 0.8554551 -0.3939400 0.7858656 -0.5091907 -0.3509137 0.4194232 -0.2589429 -0.8700761 -0.7760561 0.3511497 -0.5238622 0.9987836 -0.0413076 0.0269219 ___ Freesurfer mailing list 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.
[Freesurfer] Longitudinal processing 3 time point error
Hello, I have a dataset of patients with 3 time points each. While 2-time point processing works just fine in the longitudinal stream, when I run a base with 3 time points, the process fails and exits with errors. Please see the output below: Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.160049 Iteration(f): 2mri_robust_template(778) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 129th slice Cannot allocate memory Darwin Jamies-iMac.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 recon-all -s EB1312_61-66-77_base exited with ERRORS at Wed Sep 26 12:19:11 BST 2012 This is similar to a message on the mailing list from Liz Bowman (30 Jul 2012), in which the response was to get more memory. My command was done on a Mac with 16GB of RAM and ample disk space. I'd appreciate any help! Thanks, Jamie Kawadler ___ Freesurfer mailing list 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.
Re: [Freesurfer] Longitudinal processing 3 time point error
Hi Jamie, Three time points should not be a memory problem. You can try to run this on linux. Or you can get a new binary for the mac from our development version with several improvements and fixes including a memory leak that might have caused this. Let me know (you may want to rerun all your bases with the new version then to avoid introducing a bias, it uses cubic interpolation and should produce better results). Best Martin Kawadler, Jamie jamie.kawadler...@ucl.ac.uk wrote: Hello, I have a dataset of patients with 3 time points each. While 2-time point processing works just fine in the longitudinal stream, when I run a base with 3 time points, the process fails and exits with errors. Please see the output below: Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.160049 Iteration(f): 2mri_robust_template(778) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 129th slice Cannot allocate memory Darwin Jamies-iMac.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 recon-all -s EB1312_61-66-77_base exited with ERRORS at Wed Sep 26 12:19:11 BST 2012 This is similar to a message on the mailing list from Liz Bowman (30 Jul 2012), in which the response was to get more memory. My command was done on a Mac with 16GB of RAM and ample disk space. I'd appreciate any help! Thanks, Jamie Kawadler ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity.___ Freesurfer mailing list 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.
Re: [Freesurfer] Longitudinal processing 3 time point error
Hi Martin, Thanks for the suggestion! I'm afraid that I'm limited to the Mac - how can I get the new binary? Thanks, Jamie -- Jamie Kawadler PhD student Imaging Biophysics Unit UCL Institute of Child Health 30 Guilford Street London WC1N 1EH 02079052192 jamie.kawadler...@ucl.ac.ukmailto:jamie.kawadler...@ucl.ac.uk On 26 Sep 2012, at 13:49, Martin Reuter mreu...@nmr.mgh.harvard.edumailto:mreu...@nmr.mgh.harvard.edu wrote: Hi Jamie, Three time points should not be a memory problem. You can try to run this on linux. Or you can get a new binary for the mac from our development version with several improvements and fixes including a memory leak that might have caused this. Let me know (you may want to rerun all your bases with the new version then to avoid introducing a bias, it uses cubic interpolation and should produce better results). Best Martin Kawadler, Jamie jamie.kawadler...@ucl.ac.ukmailto:jamie.kawadler...@ucl.ac.uk wrote: Hello, I have a dataset of patients with 3 time points each. While 2-time point processing works just fine in the longitudinal stream, when I run a base with 3 time points, the process fails and exits with errors. Please see the output below: Resolution: 0 S( 256 256 256 ) T( 256 256 256 ) Iteration(f): 1 -- diff. to prev. transform: 0.160049 Iteration(f): 2mri_robust_template(778) malloc: *** mmap(size=262144) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(256, 256, 256): could not allocate 262144 bytes for 129th slice Cannot allocate memory Darwin Jamies-iMac.local 11.4.0 Darwin Kernel Version 11.4.0: Mon Apr 9 19:32:15 PDT 2012; root:xnu-1699.26.8~1/RELEASE_X86_64 x86_64 recon-all -s EB1312_61-66-77_base exited with ERRORS at Wed Sep 26 12:19:11 BST 2012 This is similar to a message on the mailing list from Liz Bowman (30 Jul 2012), in which the response was to get more memory. My command was done on a Mac with 16GB of RAM and ample disk space. I'd appreciate any help! Thanks, Jamie Kawadler Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. 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@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.
Re: [Freesurfer] how to make avgsubject for hippocampal subfields
Hi Jeong, Koen or Eugenio would know. cheers Bruce On Wed, 26 Sep 2012, BumSeok Jeong wrote: Dear Freesurfer expert, I'm interested in hippocampal subfields and performed it at each subject. If I'd rather get average hippocampal subfields (volume or surface), what I have to do? The make_average_subject command did not produce it. Does Freesurfer have average hippocampal subfield volume? Best wishes, Jeong -- ___ Freesurfer mailing list 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.
[Freesurfer] questions about recon-all pipelines
Dear FreeSurfers, I am a beginner, trying to process some 3T MPRAGE scans on my own for a project. I have a couple of simple questions 1. When I run the recon-all –autorecon1 –autorecon2 command it asks me for 001.mgz in mri/orig so I copy and paste the volume into the folder and the command works. My question is: do I need to change 001.mgz to 002, 003 an so on for every scan I process? 2. I have to process 3T scans in a .dcm format. Can I just process the scan as it is? Do I have to save the .dcm files as another format, maybe a .mnc file? thank you very much in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA ___ Freesurfer mailing list 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.
Re: [Freesurfer] questions about recon-all pipelines
Pietro You should first import your *.dcm files with the command recon-all -i first_dicom_image_name.dcm -s subjID Then when you process your data you would type recon-all -s subjID -autorecon1 -autorecon2 or whatever steps you are using. Darren On Wed, Sep 26, 2012 at 9:33 AM, pietro de rossi deross...@gmail.comwrote: Dear FreeSurfers, I am a beginner, trying to process some 3T MPRAGE scans on my own for a project. I have a couple of simple questions 1. When I run the recon-all –autorecon1 –autorecon2 command it asks me for 001.mgz in mri/orig so I copy and paste the volume into the folder and the command works. My question is: do I need to change 001.mgz to 002, 003 an so on for every scan I process? 2. I have to process 3T scans in a .dcm format. Can I just process the scan as it is? Do I have to save the .dcm files as another format, maybe a .mnc file? thank you very much in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ Freesurfer mailing list 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.
Re: [Freesurfer] questions about recon-all pipelines
Hi Pietro 1. No, you would need 002.mgz etc.. if you had more than 1 scan that you wanted to motion correct and average for that subject/session. 2. The easier way to run recon-all is to use the -i file flag, where file should be one slice in the proper dicom series (e.g. an mprage). Then you don't need to copy 001.mgz or anything, it will do everything for you. cheers Bruce On Wed, 26 Sep 2012, pietro de rossi wrote: Dear FreeSurfers, I am a beginner, trying to process some 3T MPRAGE scans on my own for a project. I have a couple of simple questions 1. When I run the recon-all ?autorecon1 ?autorecon2 command it asks me for 001.mgz in mri/orig so I copy and paste the volume into the folder and the command works. My question is: do I need to change 001.mgz to 002, 003 an so on for every scan I process? 2. I have to process 3T scans in a .dcm format. Can I just process the scan as it is? Do I have to save the .dcm files as another format, maybe a .mnc file? thank you very much in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA ___ Freesurfer mailing list 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.
Re: [Freesurfer] questions about recon-all pipelines
or you could do it all in one command with: recon-all -i first_dicom_image_name.dcm -s subjID -all cheers Bruce On Wed, 26 Sep 2012, Darren Gitelman wrote: Pietro You should first import your *.dcm files with the command recon-all -i first_dicom_image_name.dcm -s subjID Then when you process your data you would type recon-all -s subjID -autorecon1 -autorecon2 or whatever steps you are using. Darren On Wed, Sep 26, 2012 at 9:33 AM, pietro de rossi deross...@gmail.com wrote: Dear FreeSurfers, I am a beginner, trying to process some 3T MPRAGE scans on my own for a project. I have a couple of simple questions 1. When I run the recon-all ?autorecon1 ?autorecon2 command it asks me for 001.mgz in mri/orig so I copy and paste the volume into the folder and the command works. My question is: do I need to change 001.mgz to 002, 003 an so on for every scan I process? 2. I have to process 3T scans in a .dcm format. Can I just process the scan as it is? Do I have to save the .dcm files as another format, maybe a .mnc file? thank you very much in advance, Pietro -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ Freesurfer mailing list 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.
Re: [Freesurfer] question about fsaverage vs. my subjects average
On 09/26/2012 12:36 AM, Darren Gitelman wrote: Hi I have 3 questions: 1) Does it affect the stats (or does it just affect the display) if I use the fsaverage brain vs. the average of my subjects brains when running mris_preproc or when simulating the cluster statistics using mri_glmfit-sim? It will affect it some because the tessellations will be different. I have not done too many experiments to measure it, but the one I did do showed very little difference when using a subject-specific atlas. Your mileage may vary. mri_glmfit-sim expects there to be tables for each atlas. 2) I downloaded the simulations for multiple comparisons correction mult-comp_cor.tar.gz. (which I later realized were also in freesurfer/average/mult-comp-cor). How do I apply the simulations to my data (assuming I used fsaverage)? It doesn't really say on the group analysis page how to apply the *.cdf file (or I missed it). Run mri_glmfit-sim with the --cache option. Run it with --help to get more info. 3) I see on the list that mention is made of a possible symmetric template, and there is an fsaverage-sym directory in the file I downloaded. Is this template available? Yes, see http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi doug Thanks, Darren -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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] coordinate transform
Dear all, I need to transform my electrode FS volume index coordinates stored in a .mat file (see attached) in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates? Thank you, Octavian Lie. trodes.mat Description: Binary data ___ Freesurfer mailing list 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.
[Freesurfer] Should control points be removed?
Quick small question, I'm editing a few brains at the moment that have needed multiple script runs. I've added control points as necessary before each run and afterward the resulting brain will typically need either more control points added, white matter aux volume edits, or both. I'm wondering whether or not I should remove older control points after they've done their job in editing the pial and main surfaces. I only ask as I fear they may interfere with newer edits I've made and muck up the script running process, or is this not the case? best, jon Research Asst. Dept. of Radiology University of Michigan ___ Freesurfer mailing list 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.
Re: [Freesurfer] questions about recon-all pipelines
thank you very much! 2012/9/26 Bruce Fischl fis...@nmr.mgh.harvard.edu or you could do it all in one command with: recon-all -i first_dicom_image_name.dcm -s subjID -all cheers Bruce On Wed, 26 Sep 2012, Darren Gitelman wrote: Pietro You should first import your *.dcm files with the command recon-all -i first_dicom_image_name.dcm -s subjID Then when you process your data you would type recon-all -s subjID -autorecon1 -autorecon2 or whatever steps you are using. Darren On Wed, Sep 26, 2012 at 9:33 AM, pietro de rossi deross...@gmail.com wrote: Dear FreeSurfers, I am a beginner, trying to process some 3T MPRAGE scans on my own for a project. I have a couple of simple questions 1. When I run the recon-all ?autorecon1 ?autorecon2 command it asks me for 001.mgz in mri/orig so I copy and paste the volume into the folder and the command works. My question is: do I need to change 001.mgz to 002, 003 an so on for every scan I process? 2. I have to process 3T scans in a .dcm format. Can I just process the scan as it is? Do I have to save the .dcm files as another format, maybe a .mnc file? thank you very much in advance, Pietro -- Pietro De Rossi, MD --**--- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant?Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA -- Darren Gitelman, MD Northwestern University 710 N. Lake Shore Dr. Abbott 11th Floor Chicago, IL 60611 Ph: (312) 908-8614 Fax: (312) 908-5073 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/**compliancelinehttp://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. -- Pietro De Rossi, MD - Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA ___ Freesurfer mailing list 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.
Re: [Freesurfer] coordinate transform
Dear all, I need to transform my electrode FS volume index coordinates stored in a .mat file in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates? Thank you, Octavian Lie. *To follow up and simplify for a single electrode location, * ** *What I need to do is for each electrode (already localized/ projected onto the surface) to transform its volume volume index coordinate to a vertex RAS (maybe via the closest vertex volume coordinates), then to transform these vertex RAS coordinates to fsaverage template coordinate.* *I then need to calculate the geodesic and euclidean distance between the electrode location and another selected surface vertex, say (a,b,c).* *Thank you for your insight.* ** *Octavian Lie.* ___ Freesurfer mailing list 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.
Re: [Freesurfer] Should control points be removed?
Usually you don't need to remove them Bruce On Sep 26, 2012, at 1:52 PM, Jonathan Holt whats...@umich.edu wrote: Quick small question, I'm editing a few brains at the moment that have needed multiple script runs. I've added control points as necessary before each run and afterward the resulting brain will typically need either more control points added, white matter aux volume edits, or both. I'm wondering whether or not I should remove older control points after they've done their job in editing the pial and main surfaces. I only ask as I fear they may interfere with newer edits I've made and muck up the script running process, or is this not the case? best, jon Research Asst. Dept. of Radiology University of Michigan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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.
Re: [Freesurfer] coordinate transform
Hi Octavian, these types of things are generally not difficult to program, but they can be difficult to get set up correctly. If you do a search for coordinates on our wiki, it will take you to a page that explains the process. doug On 09/26/2012 02:57 PM, octavian lie wrote: Dear all, I need to transform my electrode FS volume index coordinates stored in a .mat file in surface RAS coordinates. Do you know of any matlab code that could be shared to accomplish this and generate another .mat with RAS coordinates? Thank you, Octavian Lie. *To follow up and simplify for a single electrode location, * ** *What I need to do is for each electrode (already localized/ projected onto the surface) to transform its volume volume index coordinate to a vertex RAS (maybe via the closest vertex volume coordinates), then to transform these vertex RAS coordinates to fsaverage template coordinate.* *I then need to calculate the geodesic and euclidean distance between the electrode location and another selected surface vertex, say (a,b,c).* *Thank you for your insight.* ** *Octavian Lie.* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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@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.
Re: [Freesurfer] CT Method Comparison
Sorry, I'm still a little lost. Let me see if I have it right: For a given ROI, you have a nifti file (roi.nii) in 2mm space defined on colin27. This ROI volume has a voxel value == 1 if it is in the ROI or 0 if it is out. You have a registration between roi.nii and orig.mgz You run mri_vol2surf on roi.nii to get lh.roi.mgh You run mri_cor2label (with --surf option) to convert lh.roi.mgh into lh.roi.label You run mri_label2label on lh.roi.label to map it into an individual subject You run mris_anatomical_stats on the individual lh.roi.label file Does this describe one of your processing streams correctly? If so, what is the other processing stream (given in this kind of detail)? doug On 09/25/2012 04:43 PM, Garikoitz Lerma-Usabiaga wrote: I have both. In origin, the ROI-s are 2mm volume based .nii that I convert to FS .mgh with register.dat I obtained with bbregister. -- In the case of label2label method I create the surface version with mri_vol2surf (and the correspondence is perfect), and then use mri_label2label in order to get the CT averages. -- In the case of surf2surf, I use the volume based .mgh with mri_preproc (mri_surf2surf) thanks! Gari On Tue, Sep 25, 2012 at 5:57 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: So you have ROIs in Colin27 space and you want to map them into your CT space and compute average CT intensities over them? Are the ROIs volume-based or surface-based? doug On 09/25/2012 05:09 AM, Garikoitz Lerma-Usabiaga wrote: Hi Doug, many thanks for your answer, I try to detail it more: 1.- bbregister is registering two Colin27 brains. First one is a 2mm found in spm/canonical/single_subject_T1.nii, and second one is the FS_spm_Canonical found in SurfRend distribution. It was in .COR format and I run recon-all to have a modern version of it. As they are almost the same brain the registration matrix is quite simple and the registration was perfect. This way I had exactly the same ROI-s for Colin27 in SPM and in FS (it did not work that well for fsaverage, that's why I took this approach). 2.- In any case, I have several ROI-s in Colin27 space in FS, and then when I try to obtain average CT values from my subjects I use these 2 different approaches: label2label and surf2surf. mri_anatomical_stats is run on the labels created by mri_label2label. If you think it will be of help I can send the detailed command line calls, thanks! Gari On Sat, Sep 22, 2012 at 12:47 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Gari, I'll need more information. I can't tell what you are doing. Eg, what is being registered with BBR? what is mris_anatomical_stats run on? Where does Colin27 come into it and why? doug On 09/19/2012 06:15 PM, Garikoitz Lerma-Usabiaga (Gari) wrote: Dear Freesurfers, We've been comparing 2 different methods to obtain CT averages for 4 Volume ROI-s (volume ROI-s were in Colin27 space). We've used the 40 buckner subjects for the comparisons. METHOD L2L:bbregister mri_vol2surf (mgh) mri_binarize (mgh) mri_cor2label (label) mri_label2label mris_anatomical_stats METHOD S2S: bbregister mri_vol2surf mri_preproc (mri_surf2surf) mri_segstats After performing t-test-s over the results, we can observe that the results are in many cases different. -- Is there a way to choose the best method? Which one should we use for our work and why? Many thanks again for your help, Gari PD We've tabulated a third method as well: METHOD SurfRend: Surfrend (.w) mri_surf2surf(.mgh) mri_binarize(.mgh) mri_cor2label (.label) mris_anatomical_stats ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number:
[Freesurfer] long_mris_slopes command: temporal average calculation
Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. ___ Freesurfer mailing list 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.
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity.___ Freesurfer mailing list 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.
Re: [Freesurfer] long_mris_slopes command: temporal average calculation
Hi Martin, When I used the long_mris_slopes command for the thickness, the average thickness calculated in FreeSurfer was pretty similar to averaging the values in FreeSurfer. Does this command only work thickness measures and not for volume or area? Thanks! -Shannon On Wed, Sep 26, 2012 at 2:49 PM, Martin Reuter mreu...@nmr.mgh.harvard.eduwrote: Hi Shannon You probably mean average thickness. My scripts compute the temporal average from the linear fit (at mid time), which can be differed from simply averaging values. Best Martin Shannon Kogachi skoga...@gmail.com wrote: Hi, I had a question about how the temporal average is calculated for subjects with multiple timepoints. I used the long_mris_slopes command on a longitudinal set of data. However, when I compared the average volumes calculated through this command to the average volumes calculated in excel after extracting the same vertices at the individual timepoints, these values did not match up. The average volumes calculated through long_mris_slopes were smaller. Please let me know if there is a way to explain this discrepancy. Thank you! -Shannon K. -- Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Sent from my phone, please excuse brevity. 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. -- Shannon Kogachi Clinical Research Coordinator Neuroscience and MRI Research Program Department of Medicine JABSOM, University of Hawaii 1356 Lusitana Street, 7th Floor Honolulu, HI 96813 (808) 691 - 8763 ___ Freesurfer mailing list 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.
