Re: [Freesurfer] Corpus Callosum segmentation reliability
Dear Bruce, did you see the images that I have sent you? Thanks, Alessia Giuliano From: alessia_giuli...@hotmail.it To: freesurfer@nmr.mgh.harvard.edu Date: Fri, 6 Jun 2014 06:46:29 + Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability Dear Bruce, the two subject dirs are here https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a.The original subject is s50 and the rotated one is rs50. Thank you very much for your help. Alessia Giuliano Date: Thu, 5 Jun 2014 16:27:58 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability hmmm, that is puzzling. Can you upload the two subject dirs with the rotated direction cosines and I'll take a look? thanks Bruce On Thu, 5 Jun 2014, Alessia Giuliano wrote: Dear Bruce, when I say the image was rotated in 2 I mean that I have changed the image header to reflect a new orientation, instead in 3 there was an additional image interpolation, therefore a blurring. As you said, I can understand that in the latter case things change, but how can be explained so considerable change in CC subregions volumes and in CC total volume between case 2 and 1? Moreover, we have noticed that the rostrum is sometimes included in the anterior part but othertimes not, is there a way to correct this segmentation manually? Can you give me any advices to improve the CC segmentation in order to consider the volumes of its subregions to be reliable? Thank you, Alessia Giuliano Date: Thu, 5 Jun 2014 08:30:10 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability Hi Alessia when you say the image was rotated do you mean you actually transformed the image, or you simply changed the image header to reflect a new orientation? I wouldn't think the latter would have a big effect, but the former will involve an additional image interpolation (blurring) and will definitely change things. Same question for 3. Did you include an extra interpolation? cheers Bruce On Thu, 5 Jun 2014, Alessia Giuliano wrote: Dear FreeSurefer team, in order to verify the reliability of the volumes of Corpus Callosum (CC) subregions estimated by FreeSurfer I have applied the recon-all on the same subject but in three different situations: 1. when the image was not preliminarly rotated; 2. when an initial soft rotation was manually performed with SPM; 3. when an initial rigid coregistration in MNI space was performed with SPM. Although the differences in image orientation between 1, 2 and 3 before the implementation of FreeSurfer were really small, the differences in the volumes of the CC subregions between 1, 2 and 3 are notable. How can I base on this evident variability my volumetric analysis of CC subregions? Do you have any suggestions to improve my approach to the CC segmentation? In order to make my results clear, I attach you a recapitulatory page and I send you a link to the FreeSurfer output in 1, 2 and 3 (https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a). Thank you, Alessia Giuliano ___ 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. ___ 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
Re: [Freesurfer] ?Sequence for Hippo_subfields
Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Tracula preprocessing error ( set dob0 = 1 )
Dear Freesurfer community, Whenever i try to launch the tracula preprocessing, using set dob0 = 1 and the following command line: trac-all -prep -no-isrunning -c '/home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/tracula.config It stops, giving me errors like these: niiRead(): error opening file /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi.nii.gz ERROR: reading /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_frame0.nii.gz While setting dob0 = 0 everything runs smoothly. Can you help me please? I'll attach the log + dmrirc (tracula.config) Best,Elia. -- Freesurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 Linux Distribution: Ubuntu 12.04 precise - Ubuntu 12.04.4 LTS Environment/Version: Linux king-ubuntu 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux INFO: SUBJECTS_DIR is /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D INFO: Diffusion root is /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D Actual FREESURFER_HOME /home/alberto/Desktop/freesurfer trac-preproc -c /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/scripts/dmrirc.local -log /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/scripts/trac-all.log -cmd /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/scripts/trac-all.cmd -no-isrunning #- /home/alberto/Desktop/freesurfer/bin/trac-preproc #- #@# Image corrections Thu Jun 12 12:07:07 CEST 2014 mri_convert /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.301112231117586560353.dcm /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz mri_convert /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.301112231117586560353.dcm /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.301112231117586560353.dcm... Getting Series No INFO: Found 2245 files in /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1 INFO: Scanning for Series Number 6 Scanning Directory INFO: found 2240 files in series INFO: loading series header info. RunNo = 5 INFO: sorting. INFO: (128 128 64), nframes = 35, ismosaic=0 PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix - 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000; 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000; This looks like an MGH DTI volume DTI is in non-moasic form, so cannot extract bvals/bvects FileName /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/DTI/timePoint1/1.3.12.2.1107.5.2.7.20118.301112231117586560385.dcm Identification NumarisVersyngo MR 2004A 4VA25A ScannerModel Allegra PatientName 5-001-11-MRDTI-PT-001-T00-000 Date and time StudyDate 20111223 StudyTime 120731.359000 SeriesTime124439.515000 AcqTime 123906.902499 Acquisition parameters PulseSeq ep_b0#0 Protocol DTI 2x2x2 b700 5b0 PhEncDir COL EchoNo0 FlipAngle 90 EchoTime 87 InversionTime -1 RepetitionTime9300 PhEncFOV 256 ReadoutFOV256 Image information RunNo 5 SeriesNo 6 ImageNo 1 NImageRows128 NImageCols128 NFrames 35 SliceArraylSize 64 IsMosaic 0 ImgPos128.3131 134.4756 -57.2379 VolRes 2. 2. 2. VolDim128 128 64 Vc -1. -0. 0. Vr -0. -1. -0.0087 Vs -0. -0.0087 1. VolCenter 0.3131 5.9220 5.6427 TransferSyntaxUID 1.2.840.10008.1.2 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=9300.00, TE=87.00, TI=-1.00, flip angle=90.00 i_ras = (-1, -0, 8.67362e-19) j_ras = (-0, -0.62, -0.00872654) k_ras = (-0, -0.00872654, 0.62) writing to /home/elia/scripts/Tracula/LCL/Tracula-B0-Input_zip/T13D/timePoint1/dmri/dwi_orig.nii.gz... mri_probedicom --i
Re: [Freesurfer] Corpus Callosum segmentation reliability
Hi Alessia I did, and unfortunately I'm not sure there is much I can do. One of the (long) list of engineering thing we would like to fix is how we deal with the initial nromalization of subject positioning. At the moment, the scans you sent me will be resliced differently, and it is that interpolation that causes the 5% or so differences in CC compartment volumes. sorry, Bruce On Thu, 12 Jun 2014, Alessia Giuliano wrote: Dear Bruce, did you see the images that I have sent you? Thanks, Alessia Giuliano From: alessia_giuli...@hotmail.it To: freesurfer@nmr.mgh.harvard.edu Date: Fri, 6 Jun 2014 06:46:29 + Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability Dear Bruce, the two subject dirs are here https://www.dropbox.com/sh/k1z5o0e6sq90qq0/AABx38QxKvxDhUe2lV9imaa9a. The original subject is s50 and the rotated one is rs50. Thank you very much for your help. Alessia Giuliano Date: Thu, 5 Jun 2014 16:27:58 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability hmmm, that is puzzling. Can you upload the two subject dirs with the rotated direction cosines and I'll take a look? thanks Bruce On Thu, 5 Jun 2014, Alessia Giuliano wrote: Dear Bruce, when I say the image was rotated in 2 I mean that I have changed the ima ge header to reflect a new orientation, instead in 3 there was an additional image interpolation, therefore a blur ring. As you said, I can understand that in the latter case things change, but h ow can be explained so considerable change in CC subregions volumes and in CC total volume between case 2 and 1? Moreover, we have noticed that the rostrum is sometimes included in the an terior part but othertimes not, is there a way to correct this segmentation manually? Can you give me any advices to improve the CC segmentation in order to con sider the volumes of its subregions to be reliable? Thank you, Alessia Giuliano Date: Thu, 5 Jun 2014 08:30:10 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Corpus Callosum segmentation reliability Hi Alessia when you say the image was rotated do you mean you actually transformed the image, or you simply changed the image header to reflect a new orientation? I wouldn't think the latter would have a big effect, but the former will involve an additional image interpolation (blurring) and will definitely change things. Same question for 3. Did you include an extra interpolation? cheers Bruce On Thu, 5 Jun 2014, Alessia Giuliano wrote: Dear FreeSurefer team, in order to verify the reliability of the volumes of Corpus Callosum (CC ) subregions estimated by FreeSurfer I have applied the recon-all on the same subject but in three different situations: 1. when the image was not preliminarly rotated; 2. when an initial soft rotation was manually performed with SPM; 3. when an initial rigid coregistration in MNI space was performed with SPM. Although the differences in image orientation between 1, 2 and 3 before the implementation of FreeSurfer were really small, the differences in the volumes of the CC subregions b etween 1, 2 and 3 are notable. How can I base on this evident variability my volumetric analysis of CC subregions? Do you have any suggestions to improve my approach to the CC segmentatio n? In order to make my results clear, I attach you a recapitulatory page an d I send you a link to the FreeSurfer output in 1, 2 and 3 (https://www.dropbox.com/sh/k1z5o0e6sq90 qq0/AABx38QxKvxDhUe2lV9imaa9a). Thank you, Alessia Giuliano ___ Freesurfer mailing list Fr eesur...@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The informati on 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] freeurfer manual edits
Hi Jidan for your first point, if you make both wm edits and add control points you can run -autorecon2-cp -autorecon3 as it is a superset of -autorecon2-wm. For the second one, it's hard to diagnose from the single slice. Is there white matter through-plane that is not included in the white surface or the wm.mgz? cheers Bruce On Thu, 12 Jun 2014, Jidan Zhong wrote: Dear FreeSurfer Experts, I have two questions about freesurfer troubleshoot. My subjects are people with multiple sclerosis, so for most of them I need to add control points as well as edit white matter due to lesions. As far as I know, I should add control points and do recon-all -autorecon2-cp -autorecon3 to my subject and then edit white matter, do recon-all -autorecon2-wm -autorecon3. My question is, it seems there are some repeated steps for those two recon steps, and it takes so long to run them. Is there anyway that I can save some process steps and leave it to the last recon? To be specific, can I do recon-all -autorecon2-cp only after I added control points, then do recon-all -autorecon2-wm -autorecon3 after wm edits? I think it is reasonable as after -autorecon2-cp the new white matter surface is already generated and can help to detect wm failure. But I am not sure whether this makes sense to you guys. Another question is, some of my subjects they have degenerated white matter and grey matter, so some parts get so dark that freesurfer would not include it even in the pial surface. I attached one figure for your referece. If there is no white matter detected in that unlabled part (at the top of the figure), what should I do? should I leave it or just add some white matter and control points myself to get a better segmentation and surface? [The case I show in the attachment is much better than some other cases, whose brain has some parts so dark that even I can not tell which is grey matter or white matter from my experience..] Thanks! -- Regards, Jidan ___ 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] freeurfer manual edits
FWIW: In FS 5.3, -autorecon2-cp and -autorecon2-wm invoke the exact same set of flags. (This wasn't the case in earlier versions). cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110Email: mha...@wustl.edu On 6/12/14 10:15 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jidan for your first point, if you make both wm edits and add control points you can run -autorecon2-cp -autorecon3 as it is a superset of -autorecon2-wm. For the second one, it's hard to diagnose from the single slice. Is there white matter through-plane that is not included in the white surface or the wm.mgz? cheers Bruce On Thu, 12 Jun 2014, Jidan Zhong wrote: Dear FreeSurfer Experts, I have two questions about freesurfer troubleshoot. My subjects are people with multiple sclerosis, so for most of them I need to add control points as well as edit white matter due to lesions. As far as I know, I should add control points and do recon-all -autorecon2-cp -autorecon3 to my subject and then edit white matter, do recon-all -autorecon2-wm -autorecon3. My question is, it seems there are some repeated steps for those two recon steps, and it takes so long to run them. Is there anyway that I can save some process steps and leave it to the last recon? To be specific, can I do recon-all -autorecon2-cp only after I added control points, then do recon-all -autorecon2-wm -autorecon3 after wm edits? I think it is reasonable as after -autorecon2-cp the new white matter surface is already generated and can help to detect wm failure. But I am not sure whether this makes sense to you guys. Another question is, some of my subjects they have degenerated white matter and grey matter, so some parts get so dark that freesurfer would not include it even in the pial surface. I attached one figure for your referece. If there is no white matter detected in that unlabled part (at the top of the figure), what should I do? should I leave it or just add some white matter and control points myself to get a better segmentation and surface? [The case I show in the attachment is much better than some other cases, whose brain has some parts so dark that even I can not tell which is grey matter or white matter from my experience..] Thanks! -- Regards, Jidan The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return 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] Segfault errors in tkmedit and tksurfer
Hi Joon, What version of OSX are you on and have you installed XQuartz (http://xquartz.macosforge.org/landing/)? XQuartz is required for proper tkmedit/tksurfer functionality. -Zeke On 06/11/2014 11:48 PM, Joonkoo Park, Ph.D. wrote: 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 ___ 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] Segfault errors in tkmedit and tksurfer
Hi Zeki I'm using OSX 10.7.5. And, yes I have installed XQuartz as instructed by the freesurfer installation website. Thanks! Joon -- Joonkoo Park, Ph.D. Postdoctoral Associate Center for Cognitive Neuroscience Duke University http://www.joonkoo.org/ On Thu, Jun 12, 2014 at 11:51 AM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hi Joon, What version of OSX are you on and have you installed XQuartz ( http://xquartz.macosforge.org/landing/)? XQuartz is required for proper tkmedit/tksurfer functionality. -Zeke On 06/11/2014 11:48 PM, Joonkoo Park, Ph.D. wrote: 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 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] tumor mask extreme hydrocephalus- white matter is not recognized
Hi Andrea did you try running it with -bigventricles? cheers Bruce On Thu, 12 Jun 2014, Andrea Horváth wrote: Dear Freesurfer Experts, I have two questions: 1. How can I add a previously created a tumor mask along with the mprage to improve segmentation? 2. I ran recon-all on a subject with extreme hydrocephalus. Registration to Talairach space and skull stripping were OK. However, a part of occipital white matter was not recognized as white matter even after adding control points and running recon-all -autorecon2-cp -autorecon3 due to the large ventricle as you can see in the attachment. What can you recommend to fix this problem? Thank you for your help! Cheers, Andrea ___ 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] ?Sequence for Hippo_subfields
Much appreciated Eugenio. I had read a paper where authors report using a ultra high field scanner (7T - Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference you kindly provided uses a 4T scanner... I presume using a 3T might be stretching things a bit, and I wonder whether future FS releases using T2-weighted images will accept 3T scans? Best regards and thanks again for great support you guys provide, Kev On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote: Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [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 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] Messages not appearing on Mail Archive
Hi, The messages I am sending to free sur...@nmr.mgh.harvard.edu are not showing up on the site here: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/maillist.html. But they are showing up on the digest emails that I am receiving. Is that normal? For example, the message pasted below is this morning’s digest. And my message is listed there, however, my previous two messages are not listed on the new mail archive from the website linked above. Am I doing something wrong? Appreciated, Sherryse Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-requ...@nmr.mgh.harvard.edumailto:freesurfer-requ...@nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-ow...@nmr.mgh.harvard.edumailto:freesurfer-ow...@nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than Re: Contents of Freesurfer digest... Today's Topics: 1. Re: aparc manual correction (Bruce Fischl) 2. Fwd: Extracting mean diffusivity values from diffusion data in freesurfer 5.3 (Rotem Saar) 3. ?Sequence for Hippo_subfields (Kev) 4. Displaying subset of labels on template (nmw) 5. Re: Displaying subset of labels on template (dgw) 6. Re: From NIfTI T1 to its volume cortical thickness map in MNI152 space. (Fred Sampedro) 7. Re: Displaying subset of labels on template (Bruce Fischl) 8. Re: From NIfTI T1 to its volume cortical thickness map in MNI152 space. (Bruce Fischl) 9. FW: Registration of Functional Data to the Inflated Brain (Sherryse Corrow) -- Sherryse Corrow, Ph.D. / Postdoctoral Fellow Human Vision and Eye Movement Lab Department of Ophthalmology Visual Sciences UBC/VGH Eye Care Centre 360A-2550 Willow Street Vancouver, BC, V5Z 3N9 Tel: 604-875-4111 ext 67672 Cell: 604-315-6717 sherryse.cor...@eyecarecentre.orgmailto:sherryse.cor...@eyecarecentre.org ___ 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] ?Sequence for Hippo_subfields
Yes! If Im not mistaken, ADNI is acquiring this type of data on 3T platforms. Cheers Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Thu, 12 Jun 2014 18:51:03 +0200 (CEST) Subject: Re: [Freesurfer] ?Sequence for Hippo_subfields Much appreciated Eugenio. I had read a paper where authors report using a ultra high field scanner (7T - Cho Z-H, et al. J Psychiatr Res 2010; 44: 881–886), and I notice the reference you kindly provided uses a 4T scanner... I presume using a 3T might be stretching things a bit, and I wonder whether future FS releases using T2-weighted images will accept 3T scans? Best regards and thanks again for great support you guys provide, Kev On Jun 12, 2014, at 3:49 AM, Eugenio Iglesias wrote: Dear Kev, for the subfields, people have been acquiring T2 scans with high in-plane (coronal) resolution like the ones in this paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1820772/ The subfield atlas in FreeSurfer cannot handle such scans, but we will (hopefully soon) release a version that can. Kind regards, /Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Kev schumm...@gmail.com To: Freesurfer support list Freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, June 11, 2014 8:32:33 PM Subject: [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 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
[Freesurfer] volume-based controls
I am attempting to do volume-based analysis using a data from normals as my control. Does fsaverage provide volume-based data for this purpose? Where can I find these values? Are they found anywhere outside of the freesurfer suite? Thanks in advance! ___ 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 extract significant result for each subject
Dear freesurfers, I contrast depression and control and find that patients have a lower thickness in region of inferior frontal gyrus. Now, I want to extract the data of thickness for each subject. Could you tell which command could do this? Thank you Wang Kangcheng ( New learner of 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.
