[Freesurfer] MRI book
Hi, Is there any good MRI book that teaches the basics of MRI acquisition and various types of sequences or maybe another that teaches basics of image analysis? Thanks, AJ ___ 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 get high resolution atlas on the Freesurfer ?
Hellow, Freesurfer could provide for every participant a standardized partition of the cortex into 66 regional areas. I do not know how to use freesurfer to subdivide these regional areas into a set of small and compact regions of about 1.5 cm2, resulting in high resolution atlas covering the entire cortex? Thank you!Jixin Liu ___ 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 get high resolution atlas on the Freesurfer ?
Hi Jixin mris_divide_parcellation should do the trick. You can give it the max area of a parcellation and it will keep subdividing along the primary eigen-axis until no units are above that surface area. cheers Bruce On Mon, 11 Jul 2011, ??? wrote: Hellow, Freesurfer could provide for every participant a standardized partition of the cortex into 66 regional areas. I do not know how to use freesurfer to subdivide these regional areas into a set of small and compact regions of about 1.5 cm2, resulting in high resolution atlas covering the entire cortex? Thank you! Jixin Liu ___ 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] MRI book
Hi Adil - These are books that I've found useful: http://www.amazon.com/Handbook-Pulse-Sequences-Matt-Bernstein/dp/0120928612 http://www.amazon.com/Principles-Magnetic-Resonance-Imaging-Perspective/dp/0780347234 Analysis past the image reconstruction stage is difficult to find in a single book since there are so many applications. So if you want to analyze functional MRI, diffusion MRI, etc. you'd look for a book specific to that. Hope this helps, a.y On Mon, 11 Jul 2011, Adil Javed wrote: Hi, Is there any good MRI book that teaches the basics of MRI acquisition and various types of sequences or maybe another that teaches basics of image analysis? Thanks, AJ ___ 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] Multiple frames error
Good morning Bruce, 1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer where I got the multiple frames error is a Linux, Kernel Linux 2.6.35.13-91.fc14.x86_64, GENOME 2.32.0 2). Also, when I am doing my data analysis after running the recon -all and qcache -all for my subjects, what is the best steps order to be followed. While reading the FreeSurfer Troubleshooting Reconstruction Work suggests the user to run all these steps at once before beginning to inspect the data since this allows the user to see the final complete output before deciding on any interventions.But this steps are in a different order that the one in the tutorial and also in a different order that the one described in the attached document. FreeSurfer Troubleshooting Reconstruction Work Flow:1. Source the correct version of FS 2. Set your SUBJECTS_DIR variable to your subjects directory 3. Import your data and create a subject data directory 4. Run the all the steps of recon-all 5. Check the talairach transform 6. Check the skull strip: - After adding control points run the steps -autorecon-cp (this will run -normalization, using control points, and everything else through the end of -autorecon2) and -autorecon3 (this will update all your stat tables with the new changes). - After adjusting the skullstrip, run the steps -autorecon2 and -autorecon3. 7. Check the white and pial surfaces - After editing the wm.mgz volume run the steps -autorecon2-wm (this will run -fill, using new wm.mgz volume, and everything else through the end of -autorecon2) and -autorecon3. - After editing the brainmask.mgz volume to adjust the pial surface, run the steps -autorecon-pial (this will run -finalsurfs, using new brainmask.mgz volume, and everything else through the end of -autorecon3.) 8. Check the segmentations - After editing the wm.mgz volume run the following steps: -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3. 3). Sorry for the silly question: It is possible in order to save time to do all the corrections ones at the time and then run all the autorecon in one step? Thank you for your help! Antonella ___ 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] using mri_convert with multiframe dicom
Hi All, Can mri_convert be used with multiframe dicom? In attempting to use the command that was successful on non-multiframe dicom I receive the following error: /usr/local/freesurfer/bin/mri_convert -it dicom -ot analyze 401/GL.MR.Project.401.1.20100923.103636.ench9 h.0502265032.dcm ANALYZE/Target $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 401/GL.MR.Project.401.1.20100923.103636.ench9h.0502265032.dcm... Starting DICOMRead2() dcmfile = 401/GL.MR.Project.401.1.20100923.103636.ench9h.0502265032.dcm dcmdir = 401 WARNING: tag image orientation not found Ref Series No = 401 Found 3 files, checking for dicoms WARNING: tag image orientation not found Found 1 dicom files in series. /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: 0 0 0 Vs: nan nan nan Second Sorting Counting frames nframes = 1 nslices = 1 ndcmfiles = 1 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 MRIresample(): error inverting matrix; determinant is nan, matrix is: TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -0, 0) j_ras = (-0, -0, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; Thanks. -Timothy Timothy Brown email: timo...@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Sciencefax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218 ___ 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] save label after expand boundary of region
Hi Bruce, Doug, and All: Questions on a continuing problem: When I run tksurfer, the caudalanteriorcingulate is invaded by the corpuscallosum. I edited the boundary using the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit I'm then instructed to Save the annotation: File Label Export Annotation. Probably choose a new name rather than writing over an existing file I don't need a new name - I just need to save the labels for the caudalanteriorcingulate and the corpuscallosum, which both now look correct. How/where do I do that? Here are the files in the label dir: lh.cortex.label lh.aparc.annot lh.aparc.a2009s.annot rh.cortex.label rh.aparc.annot aparc.annot.ctab rh.aparc.a2009s.annot aparc.annot.a2009s.ctab Also - I previously asked what I need to do after that to ensure accurate measurements. Bruce responded, I don't think you need recon2 since you are just changing the aparc. I believe you can just run the aparc stats step, but I'll cc Doug who might know better. Any advice on all this? Thanks, Helen Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ 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] using mri_convert with multiframe dicom
Hi Timothy you should be able to. You can use the -nth frame # switch to convert each frame individually cheers Bruce On Mon, 11 Jul 2011, Timothy Brown wrote: Hi All, Can mri_convert be used with multiframe dicom? In attempting to use the command that was successful on non-multiframe dicom I receive the following error: /usr/local/freesurfer/bin/mri_convert -it dicom -ot analyze 401/GL.MR.Project.401.1.20100923.103636.ench9 h.0502265032.dcm ANALYZE/Target $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from 401/GL.MR.Project.401.1.20100923.103636.ench9h.0502265032.dcm... Starting DICOMRead2() dcmfile = 401/GL.MR.Project.401.1.20100923.103636.ench9h.0502265032.dcm dcmdir = 401 WARNING: tag image orientation not found Ref Series No = 401 Found 3 files, checking for dicoms WARNING: tag image orientation not found Found 1 dicom files in series. /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 WARNING: tag image orientation not found First Sorting Computing Slice Direction Vs: 0 0 0 Vs: nan nan nan Second Sorting Counting frames nframes = 1 nslices = 1 ndcmfiles = 1 PE Dir = UNKNOWN (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- jpegUID: --1.2.840.10008.1.2.4-- Loading pixel data /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 /usr/pubsw/packages/vxl/1.13.0/src/core/vnl/algo/vnl_qr.txx: vnl_qrT::solve() : matrix is rank-deficien t by 2 MRIresample(): error inverting matrix; determinant is nan, matrix is: TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -0, 0) j_ras = (-0, -0, 0) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation -0.000 -0.000 nan nan; -0.000 -0.000 nan nan; 0.000 0.000 nan nan; 0.000 0.000 0.000 1.000; Thanks. -Timothy Timothy Brown email: timo...@cis.jhu.edu Computational Anatomist phone: 410.516.7551 Center for Imaging Sciencefax: 410.516.4557 Johns Hopkins University 301 Clark Hall 3400 N. Charles Street Baltimore, MD 21218 ___ 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] fscalc size mismatch error
When running fscalc, I get the following error on some of my subjects but not all of them, mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any suggestions? Thanks, Corinna ___ 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] save label after expand boundary of region
if you export it as an annotation then all the labels will be combined in one file. I think you are probably editing the ?h.aparc.annot, so you could overwrite that one if you want. The correct mri_segstats command could then be found in the subject's recon-all.log or recon-all.cmd file in the scripts dir. cheers Bruce On Mon, 11 Jul 2011, Keefe, Helen L wrote: Hi Bruce, Doug, and All: Questions on a continuing problem: When I run tksurfer, the caudalanteriorcingulate is invaded by the corpuscallosum. I edited the boundary using the instructions at: https://surfer.nmr.mgh.harvard.edu/fswiki/tksurfer_labeledit I'm then instructed to Save the annotation: File Label Export Annotation. Probably choose a new name rather than writing over an existing file I don't need a new name - I just need to save the labels for the caudalanteriorcingulate and the corpuscallosum, which both now look correct. How/where do I do that? Here are the files in the label dir: lh.cortex.label lh.aparc.annot lh.aparc.a2009s.annot rh.cortex.label rh.aparc.annot aparc.annot.ctab rh.aparc.a2009s.annot aparc.annot.a2009s.ctab Also - I previously asked what I need to do after that to ensure accurate measurements. Bruce responded, I don't think you need recon2 since you are just changing the aparc. I believe you can just run the aparc stats step, but I'll cc Doug who might know better. Any advice on all this? Thanks, Helen __ Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. __ ___ 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] fscalc size mismatch error
Hi Corinna, can you run mri_info on the two volumes and see what sizes they are? Bruce On Mon, 11 Jul 2011, Corinna Bauer wrote: When running fscalc, I get the following error on some of my subjects but not all of them, mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any suggestions? Thanks, Corinna ___ 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] fscalc size mismatch error
(forgot to cc the list)... In general, that error means the number of elements in your first input is not equal to the number of element in your second. Can you run the command and copy-paste the output into an email? Also, run 'mris_calc' with '--verbosity 10'. That will print out additional (useful) information. On 7/11/11 12:25 , Corinna Bauer wrote: When running fscalc, I get the following error on some of my subjects but not all of them, mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any suggestions? Thanks, Corinna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 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] fscalc size mismatch error
Looks like it is because one of the files has multiple frames. mri_info first file: Volume information for wm.reg.pet.mgz type: MGH dimensions: 256 x 256 x 256 x 6 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 6 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -4.7658 : x_a = 0., y_a = 0., z_a = 1., c_a = 75.9533 : x_s = 0., y_s = -1., z_s = 0., c_s = 4.7458 talairach xfm : /home/icsapo/proc/bu/013_S_0860/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 123.2342 0. 0. 1. -52.0467 0. -1. 0. 132.7458 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 123.2342 -0. -0. -1. 132.7458 -0. 1. -0.52.0467 0. 0. 0. 1. and second file: Volume information for wm.pet_binarized.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -4.7658 : x_a = 0., y_a = 0., z_a = 1., c_a = 75.9533 : x_s = 0., y_s = -1., z_s = 0., c_s = 4.7458 talairach xfm : /home/icsapo/proc/bu/013_S_0860/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 123.2342 0. 0. 1. -52.0467 0. -1. 0. 132.7458 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 123.2342 -0. -0. -1. 132.7458 -0. 1. -0.52.0467 0. 0. 0. 1. On Mon, Jul 11, 2011 at 12:51 PM, Rudolph Pienaar rudo...@nmr.mgh.harvard.edu wrote: (forgot to cc the list)... In general, that error means the number of elements in your first input is not equal to the number of element in your second. Can you run the command and copy-paste the output into an email? Also, run 'mris_calc' with '--verbosity 10'. That will print out additional (useful) information. On 7/11/11 12:25 , Corinna Bauer wrote: When running fscalc, I get the following error on some of my subjects but not all of them, mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any suggestions? Thanks, Corinna __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA 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. ___ 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] fscalc size mismatch error
Would the best solution be to average the frames of the first file or can I specify just one frame? Corinna On Mon, Jul 11, 2011 at 1:17 PM, Corinna Bauer corinna...@gmail.com wrote: Looks like it is because one of the files has multiple frames. mri_info first file: Volume information for wm.reg.pet.mgz type: MGH dimensions: 256 x 256 x 256 x 6 voxel sizes: 1., 1., 1. type: FLOAT (3) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 6 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -4.7658 : x_a = 0., y_a = 0., z_a = 1., c_a = 75.9533 : x_s = 0., y_s = -1., z_s = 0., c_s = 4.7458 talairach xfm : /home/icsapo/proc/bu/013_S_0860/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 123.2342 0. 0. 1. -52.0467 0. -1. 0. 132.7458 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 123.2342 -0. -0. -1. 132.7458 -0. 1. -0.52.0467 0. 0. 0. 1. and second file: Volume information for wm.pet_binarized.mgz type: MGH dimensions: 256 x 256 x 256 voxel sizes: 1., 1., 1. type: INT (1) fov: 256.000 dof: 0 xstart: -128.0, xend: 128.0 ystart: -128.0, yend: 128.0 zstart: -128.0, zend: 128.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1., y_r = 0., z_r = 0., c_r = -4.7658 : x_a = 0., y_a = 0., z_a = 1., c_a = 75.9533 : x_s = 0., y_s = -1., z_s = 0., c_s = 4.7458 talairach xfm : /home/icsapo/proc/bu/013_S_0860/mri/transforms/talairach.xfm Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1. 0. 0. 123.2342 0. 0. 1. -52.0467 0. -1. 0. 132.7458 0. 0. 0. 1. voxel-to-ras determinant -1 ras to voxel transform: -1. 0. 0. 123.2342 -0. -0. -1. 132.7458 -0. 1. -0.52.0467 0. 0. 0. 1. On Mon, Jul 11, 2011 at 12:51 PM, Rudolph Pienaar rudo...@nmr.mgh.harvard.edu wrote: (forgot to cc the list)... In general, that error means the number of elements in your first input is not equal to the number of element in your second. Can you run the command and copy-paste the output into an email? Also, run 'mris_calc' with '--verbosity 10'. That will print out additional (useful) information. On 7/11/11 12:25 , Corinna Bauer wrote: When running fscalc, I get the following error on some of my subjects but not all of them, mris_calc: Sorry, but I seem to have encountered an error. While checking on input filetype sizes, I found a size mismatch, i.e. len(input1)!=len(input2) Any suggestions? Thanks, Corinna __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Rudolph Pienaar, M.Eng, D.Eng / email: rudo...@nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA 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. ___ 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
Re: [Freesurfer] Error while loading qdec project file
what happens when the Load Project selection is run? when it is being saved, i expect it to exist in the tmp dir while it is being created, then it is deleted. when it is loaded, it should extract it to that directory. n. On Thu, 2011-07-07 at 09:59 +0200, Tetiana Dadakova wrote: Hi Nick, I have Mac OS X 10.6.7. Now I found the tmp folder, and can explain in more details what happens: As I save the Project File, the qdec_project_archive/qdec.table.dat is created, but it exists in /tmp only for several seconds and then disappears. Have you heard about something like this before? Do you know what the problem can be? Thank you, Tanja. On Wed, Jul 6, 2011 at 10:03 PM, Nick Schmansky ni...@nmr.mgh.harvard.edu wrote: what is your operating system? linux and mac typically have a /tmp dir, unless you're running on a cluster? n. On Wed, 2011-07-06 at 15:46 +0200, Tetiana Dadakova wrote: Dear experts, When I try to load a saved Project File, I get an error: Loading data table /tmp/qdec_project_archive/qdec.table.dat... ERROR: could not open /tmp/qdec_project_archive/qdec.table.dat Error loading the project file. I do not have any /tmp subdirectory. Should it appear when I save the Project File? Should it be in /qdec directory? Thank you, Tanja. ___ 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
[Freesurfer] Brain Volume in FreeSurfer5.1
Hi Fellow FreeSurfers, How do you calculate Brain Volume in FS5.1? In 4.5 there was the BrainSegNotVent statistic in aseg.stats, but I'm not seeing that in 5.1. I did find something about the SupraTentorialVol, but that would exclude the brainstem and cerebellum. I'm not sure if that also includes the ventricles, but that would need to be factored in as well. I did some math to compare values between 4.5 and 5.1. I took the SupraTentorialVol from 5.1, added Left-Cerebellum-White-Matter, Left-Cerebellum-Cortex, Right-Cerebellum-White-Matter, Right-Cerebellum-Cortex, and Brain-Stem. I then subtracted out the ventricles (Left/Right-Lateral-Ventricle, Left/Right-Inf-Lat-Vent, 3rd/4th/5th-Ventricle). The end result of my 5.1 volume is 51,429 voxels larger than the value from 4.5. Thanks in advance Justin -- Justin Eisenberg Candidate for B.A. in Biology | 2013 Washington University in St. Louis jeisenb...@wustl.edu 262.914.4648 ___ 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] V1 dimensions
Hello All, Is there a way to calculate the length and breadth of V1 in mm defined by the Fischl method ? How do I do it ? Thanks Ri ___ 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] interpolation during conform step of oblique acquisitions
Hi Doug, Do you have any comment regarding the easiest way to prevent interpolation of oblique acquisitions at the conform step of the FS pipeline? thanks, -MH On Thu, 2011-06-16 at 21:21 -0400, Bruce Fischl wrote: Hi Mike, the intent was to be independent of the prescription of the slices so that we could always depend on voxel coordinates having some anatomical meaning, regardless of what crazy slice orientation was prescribed. Not sure if Doug has some easier work around for you to prevent the rotation. cheers Bruce On Thu, 16 Jun 2011, Michael Harms wrote: Hi guys, I'm curious why the conform step of mri_convert (in generating mri/orig.mgz) automatically interpolates oblique acquisitions. Is this a historical legacy? Something mandated by other elements of the FS pipeline? As a consequence of this behavior, if you have an oblique acquisition that was intentionally aligned to the actual anatomy of a given subject's brain (e.g., using AutoAlign to generate a AC-PC aligned acquisition), unless one manually alters the qform in the input NIFTI file to remove the oblique components of the xform, there will be an interpolation in the generation of the mri/orig.mgz, which brings with it blurring (i.e., the same sort of concerns that prompt one to use a single MPRAGE, rather than the average of two MPRAGEs) Just curious... thanks, -MH 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
[Freesurfer] Fw: Multiple frames error
HiBruce, I 1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer where I got the multiple frames error is a Linux, Kernel Linux 2.6.35.13-91.fc14.x86_64, GENOME 2.32.0 2). Also, when I am doing my data analysis after running the recon -all and qcache -all for my subjects, what is the best steps order to be followed. While reading the FreeSurfer Troubleshooting Reconstruction Work suggests the user to run all these steps at once before beginning to inspect the data since this allows the user to see the final complete output before deciding on any interventions.But this steps are in a different order that the one in the tutorial and also in a different order that the one described in the attached document. 8. Check the segmentations - After editing the wm.mgz volume run the following steps: -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3. Thank you for your help! Antonella ___ 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] Fw: Multiple frames error
Hi Antonella, usually we run everything then go back and check. I'll leave 1) for Nick and Krish. cheers Bruce On Mon, 11 Jul 2011, Antonella Kis wrote: Hi Bruce, I 1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer where I got the multiple frames error is a Linux, Kernel Linux 2.6.35.13-91.fc14.x86_64, GENOME 2.32.0 2). Also, when I am doing my data analysis after running the recon -all and qcache -all for my subjects, what is the best steps order to be followed. While reading the FreeSurfer Troubleshooting Reconstruction Work suggests the user to run all these steps at once before beginning to inspect the data since this allows the user to see the final complete output before deciding on any interventions.But this steps are in a different order that the one in the tutorial and also in a different order that the one described in the attached document. 8. Check the segmentations - After editing the wm.mgz volume run the following steps: -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3. Thank you for your help! Antonella ___ 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] Nipype 0.4 release
Dear all, I am delighted to announce release of Nipype version 0.4. Nipype, an open-source, community-developed initiative under the umbrella of NiPy, is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. Nipype provides an environment that encourages interactive exploration of algorithms from different packages (e.g., SPM, FSL, FreeSurfer, Camino, AFNI, Slicer), eases the design of workflows within and between packages, and reduces the learning curve necessary to use different packages. Nipype is creating a collaborative platform for neuroimaging software development in a high-level language and addressing limitations of existing pipeline systems. This release brings plenty of improvements. Among the most important are: new modular executions system (direct support for PBS, SGE, and multi-processing), support for Camino, Camino2Trackvis and Connectome Viewer, improved parallel performance of MapNode, and growing collection of ready to use pipelines (have a look at nipype.workflows). Grab it from https://github.com/nipy/nipype/tarball/0.4 For support please use our mailing list: nipy-us...@googlegroups.com Full changelog: * API: Timestamp hashing does not use ctime anymore. Please update your hashes by running workflows with updatehash=True option NOTE: THIS IS THE DEFAULT CONFIG NOW, so unless you updatehash, workflows will rerun * API: Workflow run function no longer supports (inseries, createdirsonly). Functions used in connect string must be pickleable * API: SPM EstimateContrast: ignore_derivs replaced by use_derivs * API: All interfaces: added new config option ignore_exception * API: SpecifModel no longer supports (concatenate_runs, output_specs). high_pass_filter cutoff is mandatory (even if its set to np.inf). Additional interfaces SpecifySPMModel and SpecifySparseModel support other types of data. * API: fsl.DTIFit input save is now called save_tensor * API: All inputs of IdentityInterfaces are mandatory by default. You can turn this off by specifying mandatory_inputs=False to the constructor. * API: fsl FILMGLS input autocorr_estimate is now called autocorr_estimate_only * API: fsl ContrastMgr now requires access to specific files (no longer accepts the result directory) * API: freesurfer.GLMFit input surf is now a boolean with three corresponding inputs -- subject_id, hemi, and surf_geo * ENH: All commandline interfaces display stdout and stderr * ENH: All interfaces raise exceptions on error with an option to suppress * ENH: Supports a plugin interface for execution (current support for multiprocessing, IPython, SGE, PBS) * ENH: MapNode runs in parallel under IPython, SGE, MultiProc, PBS * ENH: Optionally allows keeping only required outputs * ENH: New interface: utility.Rename to change the name of files, optionally using python string-formatting with inputs or regular expressions matching * ENH: New interface: freesurfer.ApplyMask (mri_mask) * ENH: New FSL interface -- SwapDimensions (fslswapdim) * ENH: Sparse models allow regressor scaling and temporal derivatives * ENH: Added support for the component parts of FSL's TBSS workflow (TBSSSkeleton and DistanceMap) * ENH: dcm2nii interface exposes bvals, bvecs, reoriented and cropped images * ENH: Added several higher-level interfaces to the fslmaths command: - ChangeDataType, Threshold, MeanImage, IsotropicSmooth, ApplyMask, TemporalFilter DilateImage, ErodeImage, SpatialFilter, UnaryMaths, BinaryMaths, MultiImageMaths * ENH: added support for networx 1.4 and improved iterable expansion * ENH: Replaced BEDPOSTX and EddyCurrent with nipype pipelines * ENH: Ability to create a hierarchical dot file * ENH: Improved debugging information for rerunning nodes * ENH: Added 'stop_on_first_rerun' option * ENH: Added support for Camino * ENH: Added support for Camino2Trackvis * ENH: Added support for Connectome Viewer * BF: dcm2nii interface handles gzipped files correctly * BF: FNIRT generates proper outputs * BF: fsl.DTIFit now properly collects tensor volume * BF: updatehash now removes old result hash file Enjoy! Chris Gorgolewski on behalf of Team Nipype ( https://www.ohloh.net/p/nipype/contributors ) ___ 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] Creation of normalized cortical regions of interest
Hi Wang, you can use mris_divide_parcellation. cheers Bruce On Fri, 8 Jul 2011, ??? wrote: Hi,freesurfers: Recently,I read a paper which used freesurfer to processed their data,this is the paper's link:http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0060159 In this paper,the antor said : One of the critical steps of the whole procedure was to partition the participants' cortex into ROIs located in an identical topographic position for each participant despite interindividual anatomical variation. We used Freesurfer to register a labeled mesh from an average brain onto the brain of each individual participant, where each label corresponded to one of 66 anatomical cortical regions . This output provided for every participant a standardized partition of the cortex into 66 regional areas. In a second step, each of these regional areas were subdivided on the Freesurfer average brain into a set of small and compact regions of about 1.5 cm2, resulting in 998 ROIs covering the entire cortex. This subdivision was then registered on the individual brain using the same transformation as for the 66 regional areas thus maintaining the topological constraints of mapping. Consequently, the resulting partitions of the cortex into 66 and 998 ROIs were in anatomically closely matched positions for all participants So,I wander how can we subdivided the 66 ROIs into 998 ROIs? Thanks, wang ___ 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] Fw: Multiple frames error
this page has some notes on a particular tksurfer problem: https://surfer.nmr.mgh.harvard.edu/fswiki/TksurferDisplayProblems not sure if this is what you are encountering. n. On Mon, 2011-07-11 at 15:41 -0400, Bruce Fischl wrote: Hi Antonella, usually we run everything then go back and check. I'll leave 1) for Nick and Krish. cheers Bruce On Mon, 11 Jul 2011, Antonella Kis wrote: Hi Bruce, I 1). My LNX3 the only one which is working is a Fedora Linux, Kernel Linux 2.6.32.23-170.fc12.x86_64, GENOME 2.28.2 LNX2 where I get the weird surface display is a Linux CENTOS x86_64, GENOME 2.16.0 The Analyst computer where I got the multiple frames error is a Linux, Kernel Linux 2.6.35.13-91.fc14.x86_64, GENOME 2.32.0 2). Also, when I am doing my data analysis after running the recon -all and qcache -all for my subjects, what is the best steps order to be followed. While reading the FreeSurfer Troubleshooting Reconstruction Work suggests the user to run all these steps at once before beginning to inspect the data since this allows the user to see the final complete output before deciding on any interventions.But this steps are in a different order that the one in the tutorial and also in a different order that the one described in the attached document. 8. Check the segmentations - After editing the wm.mgz volume run the following steps: -normalization -maskbfs -segmentation -autorecon2-wm -autorecon3. Thank you for your help! Antonella ___ 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] New version and workflow
Hello Freesurfer users and experts, We already run 55 subjects with Freesurfer 5.0 and wish now to increase our sample size up to 200 and are now deciding whether to run everybody again with Freesurfer 5.1 or just go on with the previous version. We are doing subcortical analysis (amygdala) and hopefully cortical analysis (correlations with behavioural results), on Siemens 3T. I have 2 questions relative to this issue : - To what extend should the results be more accurate or reliable (I read in the release note that 3T data is now better handled) ? I run 3 subjects on boths versions and compared aseg stats, most results were very close except for a few that were highly discrepant (ex left amygdala and hippocampus for 1 subject were much smaller with FS 5.1). What could explain this? - I also noticed on the web site that the recommended workflow had been updated. Is this linked to the new release (if less or no editing is needed, checking the output only after recon-all -all would obviously save time...)? Is less need for editing expected with the new release? Or is less editing now advised (Less is more)? Thanks in advance for any advice! Myriam Siefert ___ 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] New version and workflow
Hi Myriam we are continually working to improve accuracy and robustness. Amygdala is of course pretty difficult. Did you look at the discrepant case? If so, which one was visually more accurate? And yes, we expect that somewhat less editing is required in 5.1. There is also an array of new functionality in 5.1 that wasn't in 5.0 (e.g. hippocampal field segmentation, automated tractography, combined volume/surface segmentation, improved longitudinal, etc) cheers Bruce On Mon, 11 Jul 2011, Myriam Siefert wrote: Hello Freesurfer users and experts, We already run 55 subjects with Freesurfer 5.0 and wish now to increase our sample size up to 200 and are now deciding whether to run everybody again with Freesurfer 5.1 or just go on with the previous version. We are doing subcortical analysis (amygdala) and hopefully cortical analysis (correlations with behavioural results), on Siemens 3T. I have 2 questions relative to this issue : - To what extend should the results be more accurate or reliable (I read in the release note that 3T data is now better handled) ? I run 3 subjects on boths versions and compared aseg stats, most results were very close except for a few that were highly discrepant (ex left amygdala and hippocampus for 1 subject were much smaller with FS 5.1). What could explain this? - I also noticed on the web site that the recommended workflow had been updated. Is this linked to the new release (if less or no editing is needed, checking the output only after recon-all -all would obviously save time...)? Is less need for editing expected with the new release? Or is less editing now advised (Less is more)? Thanks in advance for any advice! Myriam Siefert ___ 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] mri_convert and orientation
Hi all, I have a nifti file f.nii whose size is 80*80*60*266, (266 is the TRs). Using mri_info f.nii, I can see that its orientation is is PIL. I want to change it to RPI. I do the following: mri_conver --in_orientation PIL --out_orientation RPI -i f.nii -o f.rpi.nii It give me f.rpi.nii, which has an orientaion of RPI. The problem is that f.rpi.nii is 80*80*60. It contains only one volume. How can I get a reoriented volume that has the same size as the original 80*80*60*266? Many thanks. Yang ___ 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.
