[Freesurfer] aparc manual correction
Dear FreeSurfer users, can anybody tell me if and how it is possible to manually correct an uncorrect parcellation of the CC, i.e. if the rostrum is uncorrectly assigned to the CC_Mid_Anterior label instead of the CC_Anterior label? Thank you. Best Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php http://icbn.uniud.it/tiki-index.php* ___ 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] aparc manual correction
Hi Elisa, you should be able to draw in the correct segmentation in either freeview or tkmedit cheers Bruce On Wed, 11 Jun 2014, elisa veronese wrote: Dear FreeSurfer users, can anybody tell me if and how it is possible to manually correct an uncorrect parcellation of the CC, i.e. if the rostrum is uncorrectly assigned to the CC_Mid_Anterior label instead of the CC_Anterior label? Thank you. Best Elisa -- Elisa Veronese - PhD Research Unit on Brain Imaging and Neuropsychology (RUBIN) Inter-University Center for Behavioral Neurosciences (ICBN) University of Udine and University of Verona, Italy ICBN Website: http://icbn.uniud.it/tiki-index.php ___ 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] ?Sequence for Hippo_subfields
Dear FS experts, I'm in the designing stage of a neuroimaging project on a 3T scanner, and I'm interested in looking at structural information on hippocampus (including subfields). In addition to the MPRAGE or IR-SPGR, is it worth running a specific acquisition sequence geared to get the most out of all the hippocampus structural measures? Thanks and regards, Kev ___ 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] Displaying subset of labels on template
Greetings, Is there any way to display just a subset of cortical labels onto one of the Freesurfer template brains (e.g., cvs_avg35) rather than all that are listed in lh.aparc.annot? I'm interested in loading frontal pole, superior frontal, superior parietal, etc onto a standard Freesurfer brain. My first thought was to create a new lh.aparc.annot file; however, I am having trouble editing it. Any thoughts? Thanks, Nate ___ 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] Displaying subset of labels on template
You could use mri_annotation2label Then just load only the labels you care about. HTH D On Wed, Jun 11, 2014 at 3:11 PM, nmw njmed...@illinois.edu wrote: Greetings, Is there any way to display just a subset of cortical labels onto one of the Freesurfer template brains (e.g., cvs_avg35) rather than all that are listed in lh.aparc.annot? I'm interested in loading frontal pole, superior frontal, superior parietal, etc onto a standard Freesurfer brain. My first thought was to create a new lh.aparc.annot file; however, I am having trouble editing it. Any thoughts? Thanks, Nate ___ 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 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] From NIfTI T1 to its volume cortical thickness map in MNI152 space.
Hi again, Any suggestions at least conceptual to the path I should follow to obtain cortical thickness volumetric data in MNI space? Thanks! On Sun, Jun 8, 2014 at 6:54 PM, Fred Sampedro fredsampe...@gmail.com wrote: Dear FreeSurfer experts, I am interested in analyzing group differences in cortical thickness with an application-specific GLM model that is build to work on MNI152 volume data. For that, my plan is to obtain a cortical thickness volume in MNI152 space for each of my MRI scans. My input data are nifti T1 scans. Here is my pipeline proposal for each T1 scan: INPUT: FOO_SUBJECT.nii FREESURFER CALLS (in $SUBJECTS_DIR): 1) recon-all -i FOO_SUBJECT.nii -subjid foosub 2) recon-all -all -subjid foosub 3) mri_surf2vol --surfvalpath /foosub/surf/lh.thickness --o foosub_cth_vol_lh #(?) 4) mri_surf2vol --surfvalpath /foosub/surf/rh.thickness --o foosub_cth_vol_rh #(?) 5) #should I merge lh and rh (?) how (?) let it be foosub_cth_vol 6) fslregister --s foosub_cth_vol --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat #should I convert it to MNI152 space (?) and how (?) 6) mri_fwhm --i foosub_cth_vol --o smoothed_foosub_cth_vol # should I smooth it (?) and how (?) OUTPUT to statistical analysis: smoothed_foosub_cth_vol (?) As you can see, I am pretty new to freesurfer and I have a lot of technical and conceptual gaps in this pipeline. Any advice on how to robustly accomplish this task would be much appreciated, as well as any advice regarding whether it would be a bad idea to try to carry out this kind of procedure in the first place. The context of the application is to apply the same ad-hoc statistical groupal analysis to PET, VBM GM, and cortical thickness data for all subjects. Thanks a lot in advance, Fred Sampedro ___ 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] Displaying subset of labels on template
Hi Nate you can use mri_annotation2label to create separate label files, then load whetever you want. cheers Bruce On Wed, 11 Jun 2014, nmw wrote: Greetings, Is there any way to display just a subset of cortical labels onto one of the Freesurfer template brains (e.g., cvs_avg35) rather than all that are listed in lh.aparc.annot? I'm interested in loading frontal pole, superior frontal, superior parietal, etc onto a standard Freesurfer brain. My first thought was to create a new lh.aparc.annot file; however, I am having trouble editing it. Any thoughts? Thanks, Nate ___ 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] From NIfTI T1 to its volume cortical thickness map in MNI152 space.
Hi Fred can you explain what cortical thickness volumetric data in MNI space means? Thickness is not a volumetric quantity - it is undefined for much of the volume (the part that is not in cortex). You could sample the thickness into the ribbon, but what you would find is that the individual subject ribbons don't line up in MNI space cheers Bruce On Wed, 11 Jun 2014, Fred Sampedro wrote: Hi again, Any suggestions at least conceptual to the path I should follow to obtain cortical thickness volumetric data in MNI space? Thanks! On Sun, Jun 8, 2014 at 6:54 PM, Fred Sampedro fredsampe...@gmail.com wrote: Dear FreeSurfer experts, I am interested in analyzing group differences in cortical thickness with an application-specific GLM model that is build to work on MNI152 volume data. For that, my plan is to obtain a cortical thickness volume in MNI152 space for each of my MRI scans. My input data are nifti T1 scans. Here is my pipeline proposal for each T1 scan: INPUT: FOO_SUBJECT.nii FREESURFER CALLS (in $SUBJECTS_DIR): 1) recon-all -i FOO_SUBJECT.nii -subjid foosub 2) recon-all -all -subjid foosub 3) mri_surf2vol --surfvalpath /foosub/surf/lh.thickness --o foosub_cth_vol_lh #(?) 4) mri_surf2vol --surfvalpath /foosub/surf/rh.thickness --o foosub_cth_vol_rh #(?) 5) #should I merge lh and rh (?) how (?) let it be foosub_cth_vol 6) fslregister --s foosub_cth_vol --mov /path/to/TT_avg152T1.nii --reg TT_avg152T1_to_fsaverage.dat #should I convert it to MNI152 space (?) and how (?) 6) mri_fwhm --i foosub_cth_vol --o smoothed_foosub_cth_vol # should I smooth it (?) and how (?) OUTPUT to statistical analysis: smoothed_foosub_cth_vol (?) As you can see, I am pretty new to freesurfer and I have a lot of technical and conceptual gaps in this pipeline. Any advice on how to robustly accomplish this task would be much appreciated, as well as any advice regarding whether it would be a bad idea to try to carry out this kind of procedure in the first place. The context of the application is to apply the same ad-hoc statistical groupal analysis to PET, VBM GM, and cortical thickness data for all subjects. Thanks a lot in advance, Fred Sampedro ___ 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] Dura correction using MEMPRAGE vs bandwidth-matched FLAIR
Hi,We are at the start of a study on TBI, in which we’re obtaining MEMPRAGE and T2-SPACE-FLAIR images (the images are obtained in Lunder 6 scanner, and I wonder if I can find T1 FLAIR matched sequences for morphormetry on that scanner). The pixel size of the MEMPRAGE sequence is 1mm isotropic, while the one for T2-SPACE-FLAIR is 0.5 x 0.5 x 1mm; they’re not bandwidth matched either (I’ve attached the details of the sequences we’re using). I just wanted to know if we should make changes to our T2-SPACE-FLAIR sequence and match it with the MEMPRAGE sequence to feed the FLAIR images into recon-all for dura correction, or if we should leave the T2-SPACE-FLAIR sequence as it is and use the four echoes of MEMPRAGE for dura correction (I mean, is dura correction using different echoes of MEMPRAGE as good as feeding FLAIR images into recon-all?)Thank you very much,Emad Emad Ahmadi, MD---Postdoc Research FellowDepartment of RadiologyMassachusetts General HospitalHarvard Medical School25 New Chardon Street, Suite 400Boston, MA 02114Tel: 617 726 5237Email: e...@nmr.mgh.harvard.edu SIEMENS MAGNETOM Skyra syngo MR D13 - \\USER\RESEARCH\Gupta_Research\Main Sequences\MEMPRAGE_IPAT3 TA:4:28 PAT:3 Voxel size:1.0Ã1.0Ã1.0 mm Rel. SNR:1.00 :tfl_me - Properties Prio Recon Off Load to viewer On Inline movieOff Auto store images On Load to stamp segments Off Load images to graphic segments Off Auto open inline displayOff Wait for user to start On Start measurements single Routine Nr. of slab groups 1 Slabs 1 Dist. factor50 % PositionIsocenter Orientation Sagittal Phase enc. dir. A P AutoAlign --- Phase oversampling 0 % Slice oversampling 0.0 % FoV read256 mm FoV phase 100.0 % Slice thickness 1.00 mm TR 2530.0 ms TE 11.69 ms Averages1 Concatenations 1 Filter Prescan Normalize Coil elements HEA;HEP Contrast Magn. preparation Non-sel. IR TI 1100 ms Flip angle 7.0 deg Fat suppr. None Water suppr.None Averaging mode Long term Measurements1 Reconstruction Magn./Phase Multiple series Each measurement Resolution Base resolution 256 Phase resolution100 % Phase partial Fourier Off Interpolation Off PAT modeGRAPPA Accel. factor PE3 Ref. lines PE 32 Reference scan mode Integrated Image FilterOff Distortion Corr.Off Accel. factor 3D1 Unfiltered images Off Prescan Normalize On Normalize Off B1 filter Off Raw filter Off Elliptical filter Off Slice resolution100 % Slice partial Fourier Off Geometry Nr. of slab groups 1 Slabs 1 Dist. factor50 % PositionIsocenter Phase enc. dir. A P Phase oversampling 0 % Slice oversampling 0.0 % Slices per slab 176 Multi-slice modeSingle shot Series Interleaved Nr. of sat. regions 0 Position mode
[Freesurfer] Segfault errors in tkmedit and tksurfer
Hello, I've used FreeSurfer previously on a linux machine (from a previous lab). Now, I have just installed it on a Mac OSX, using the freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg version. I followed all the instructions on the installation page. However, there were segfault errors when running both tkmedit and tksurfer as follows: dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tkmedit tkmedit started: Wed Jun 11 23:28:05 2014 /Applications/freesurfer/tktools/tkmedit.bin bert orig.mgz $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /Applications/freesurfer Set subject home dir to /Applications/freesurfer/subjects/bert Using interface file /Applications/freesurfer/tktools/tkmedit.tcl Segfault Setting global interpreter xDebug stack (length: 2) 01: main() 01: Setting global interpreter 00: 00: dyn-152-3-184-222:freesurfer joonkoopark$ more .xdebug_tksurfer Segfault Initializing glut xDebug stack (length: 1) 00: 00: Initializing glut Segfault Initializing glut dyn-152-3-184-222:freesurfer joonkoopark$ Any idea what went wrong and how to fix it? Thank you! Joon ___ 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] protocol question
Dear Freesurfer Experts, I am trying to better understand what regions of the hippocampal formation are meant to be included in the hippocampal label (e.g. inclusion of the alveus/fornix, lateral boundaries around the subiculum, superior boundaries in the tail, etc.). Has the protocol used to manually segment the hippocampus for the Freesurfer atlases been described in detail somewhere? I cannot seem to locate a specific reference. Thanks Joshua ___ 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] Freesurfer installation problem
Nick, Thanks very much. I will do as per your suggestion. I am new to Linux and Ubuntu. If I am not bothering you too much. I read an article where they compared the results from Freesurfer's different versions and about using different OS and concluded saying that use the same version and do not upgrade while in the middle of the study. My collaborators are using Freesurfer 5.0 and I will be helping them in processing the data (sharing the data processing and analysis) so is it ok to use use 5.3.0 or 5.0 is recommended. Thanks very much again Venkat On Wed, Jun 11, 2014 at 12:50 AM, Nick Schmansky, MGH ni...@nmr.mgh.harvard.edu wrote: Venkat, Your system appears to be 32bit distribution, as indicated by 'i686' in your output string, but the freesurfer you installed is 64b, indicated by 'x86_64' in our filename. So you will need the 32b dist: freesurfer-Linux-centos4-stable-pub-v5.3.0.tar.gz Also, v5.0.0 is pretty old, I'd recommend v5.3.0. Nick On Tue, 2014-06-10 at 13:23 +0530, Venkateswaran Rajagopalan wrote: Dear All, I looked into the archives extensively but could not find a solution to my problem. I am having Ubuntu Linux administrator-HP-Pro-3330-MT 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:08:14 UTC 2014 i686 i686 i686 GNU/Linux. I tried installing freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0.tar.gz. But I get the following error message mri_convert /usr/local/freesurfer/bin/mri_convert: Exec format error. Binary file not executable. tkmedit /usr/local/freesurfer/tktools/tkmedit.bin: Exec format error. Binary file not executable. I followed the instruction steps as given in freesurfer wiki. What am I doing wrong here?. Is there a installation wiki page for giving guidelines for ubuntu freesurfer installation. Thanks, any help will be greatly appreciated as I am trying to install freesurfer for the past 3 days without success. Thanks Venkat ___ 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. ___ 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.
