[Freesurfer] Before recon-all, is it necessary to set origin of the image?
Dear all, I'm new on FreeSurfer. I want to calculate cortical thickness, hippocampus volume from MRI images (obtained from ADNI). After installation, I tried recon-all. Only this process, can I obtain cortical thickness and hippocampus volume? And someone told me that I have to set origin of the image of each case using SPM program. I want to know that is it necessary? Thank you? for your kind attention Best Regards, Ngoak? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tracula_average_average center
Hi Anastasia, One of Tracula's output is the pathstats.overal.txt and in this file we have a list of numbers. Kindly what is the difference between the metrics average and the metrics average center also which one do you recommend to do statistic? Thanks, Mohamad ___ 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] permission denied
Hi I’ve previously encountered the same error. I’ve also tried to change permission but that didn’t really work out for me. I have fixed it by installing libjpeg62-dev: Maybe the following command could fix your problem too? sudo apt-get install libjpeg62-dev Hope this might work for you? Cheers Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be On 31 Oct 2014, at 16:35, zkauf...@nmr.mgh.harvard.edu wrote: Yes, please try running as root and get back when you have the chance. This is a very odd issue and your results when running as root will provide insight. -Zeke Hi Z K, Yes I am sure as I have tried the same MPRGAE image on all 16 PCs. The one installed with the latest freesurfer version did not work while others finished the processing in a reasonable processing time and I got the results. Also, I have a PC at my office installed with the latest freesurfer version and it works fine. So I have two PCs installed with the latest Freesurfer (one of them which does not work is in the lab). To summarize: All PCs (16 PCs in the lab and 1 in my office) are installed with latest Ubuntu version 14.04 64 bits 15 PCs in the lab are installed with freesurfer 5.0.0 version 1 PC in the lab is installed with the latest freesurfer version (does not work, permission denied) 1 PC in my office is installed with the latest freesurfer version (works fine) All these PCs have Ubuntu 14.04 64bit installed on them. No, I am not using any vitual machine. Regarding the root user, I will try it on Sunday as I am away for a couple of days. Many thanks for your continuous support. Ali On Thu, Oct 30, 2014 at 6:34 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Ali, First, are you ABSOLUTELY sure the PCs running freesurfer v5.0 are working properly? I am under the impression that versions of freesurfer pre-version 5.3 will not work on newer linux distributions? In regards to your current permision denied issue... What happens if you try and run tkmedit as root user? Also, you not using virtual machine setup are you? -Zeke On 10/30/2014 06:27 AM, Ali Radaideh wrote: It does not work. This is really strange On Thu, Oct 30, 2014 at 12:53 AM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: I beleive it should have a lower case X, as in: chmod -R a+x freesurfer/bin -Zeke On 10/28/2014 01:19 AM, Ali Radaideh wrote: Dear Douglas Thanks for your reply. unfortunatey I still get the same error. Here is the terminal output. Is there anything else I can do? freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni FSL_DIR /usr/local/fsl imaging@imaging-ThinkCentre-23:~$ tcsh imaging-ThinkCentre-23:~ tkmedit /usr/local/freesurfer/bin/tkmedit: Permission denied. imaging-ThinkCentre-23:~ On Mon, Oct 27, 2014 at 5:21 AM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Try chmod -R a+X freesurfer/bin On 10/26/14 1:57 PM, Ali Radaideh wrote: Dear FreeSurfer users, I am using freesurfer on 16 PCs (Ubuntu 14.04 64 bit). One of the PCs has the latest version of freesurfer 5.3.0 while the others have the version 5.0.0. The PC that is installed with the latest version freesurfer 5.3.0 does not allow me to run any command and everytime I try a command such such as tkmedit i get the following error /usr/local/freesurfer/bin/tkmedit: permission denied. I have tried to change the permission settings sudo chown -R imaging:imaging freesurfer but did not work. Any ideas why is this happening although I have done the same thing to other PCs and they are working fine. âThanks in advance, Aliâ -- /Ali M. Al-Radaideh. PhD Assistant Professor Head of Department of Medical Imaging Vice Dean of the Faculty of Allied Health Sciences The Hashemite University, Zarqa, Jordan W.phone +962 5 390 ext.5422, 5355, 5364 Email: ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ Freesurfer mailing
[Freesurfer] longitudinal data processing
Dear FS-experts Is there any command that I can use for caching my preprocessed data in the recon-all longitudinal stream, since this is possible through adding the -qcache option in the cross-sectional pipeline. Or maybe this is already automatically done without adding any option to the command? Thank you Greeting Robby Robby De Pauw, drs. Ghent University Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be ___ 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] freeview fault: PETSC Error ...
I recently downloaded and installed freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz . I had been running this version previously but had to reload everything due to a disk crash. recon-all -all goes to completion with no errors. freeview starts up fine but fails on loading a volume file with the PETC error listed below. I found several references to this error in the archive but no resolution for my problem. Any thoughts would be welcome - thanks. [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: Unknown Name on a linux-gnu named BTRC-Server01 by kriegerd Tue Nov 4 06:55:17 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text ___ 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] prefrontal cortex label
thank you. which labels are normally included as prefrontal cortex for freesurfer purposes? On Thu, Oct 23, 2014 at 5:04 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You can use mri_annotation2label to break up the annotation into individual labels, then use mris_label2annot to recombine selected labels into an annotation or use mri_merge_label to merge them into a single label. All you have to do is decide with labels define prefontal doug On 10/23/2014 10:25 AM, Anna Jonsson wrote: Dear group, Is there a way to create a prefrontal cortex label in fresurfer? if so, please tell me the exact steps to do so, I am very confused. Thank you, Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Before recon-all, is it necessary to set origin of the image?
Hi Ngoaka no, you don't need to set the origin of the image. Just point recon-all at a single slice from the correct dicom series (of a highres T1-weighted scan) with the -i full path and file name of dicom slice -all -s subject id that you pick and you should be good to go cheers Bruce On Tue, 4 Nov 2014, CHONNIKAN JONGKREANGKRAI wrote: Dear all, I'm new on FreeSurfer. I want to calculate cortical thickness, hippocampus volume from MRI images (obtained from ADNI). After installation, I tried recon-all. Only this process, can I obtain cortical thickness and hippocampus volume? And someone told me that I have to set origin of the image of each case using SPM program. I want to know that is it necessary? Thank you for your kind attention Best Regards, Ngoak ___ 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] Quality of surface-based alignment
Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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] Before recon-all, is it necessary to set origin of the image?
Dear Bruce, Thank you for quick answer. I can use .nii file instead of dicom, right? Best Regards, Ngoak On 4 พ.ย. 2557, at 22:06, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ngoaka no, you don't need to set the origin of the image. Just point recon-all at a single slice from the correct dicom series (of a highres T1-weighted scan) with the -i full path and file name of dicom slice -all -s subject id that you pick and you should be good to go cheers Bruce On Tue, 4 Nov 2014, CHONNIKAN JONGKREANGKRAI wrote: Dear all, I'm new on FreeSurfer. I want to calculate cortical thickness, hippocampus volume from MRI images (obtained from ADNI). After installation, I tried recon-all. Only this process, can I obtain cortical thickness and hippocampus volume? And someone told me that I have to set origin of the image of each case using SPM program. I want to know that is it necessary? Thank you for your kind attention Best Regards, Ngoak ___ 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
Re: [Freesurfer] Fwd: Underinclusion of Gray Matter
You could also add a lot more voxels to the wm.mgz (beyond what is wm) and depending on the source of the problem, that could fix it. On Mon, 3 Nov 2014, Bruce Fischl wrote: Hi Christina it's tough to tell from just a single image, but it looks to me like you are missing a bunch of white matter. Can you tell us more about the scan? The typical way you would fix this is by setting some thresholds in mris_make_surfaces using the expert options. Probably max_csf should be lower. If you upload the subject we will take a look cheers Bruce On Mon, 3 Nov 2014, Christina Chen wrote: Hi, Are there any ways to fix underinclusion of gray matter cortical edges when the white matter is fine? Attached is a picture. Thanks, Christina ___ 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] longitudinal data processing
Hi Robby, depends on what you are trying to achieve. The first stats model we implemented was the 2-stage model (with a linear fit inside each subject and then a cross sectional comparison of the atrophy rates, ie. slopes of the fit). For the first step the surface data (within-subject) is already in a common space (although not smoothed yet) and no qcache is needed and for the second step it cannot be done without first doing the first step. Now we also have tools for linear mixed effects modelling. For that we need all data (all time points from all subjects) in the fsaverage space. Try using the -qcache command on the longitudinal directories (e.g. together with the --long flag etc). That should do the trick. Best, Martin On 11/04/2014 07:27 AM, Robby De Pauw wrote: Dear FS-experts Is there any command that I can use for caching my preprocessed data in the recon-all longitudinal stream, since this is possible through adding the -qcache option in the cross-sectional pipeline. Or maybe this is already automatically done without adding any option to the command? Thank you Greeting Robby Robby De Pauw, drs. *Ghent University* Department of Physiotherapy and Rehabilitation Sciences 3B3 De Pintelaan 185 B-9000 Ghent robby.dep...@ugent.be mailto:robby.dep...@ugent.be ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ 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] Quality of surface-based alignment
What criteria would you use to determine one alignment was better than another? Peace, Matt. From: Caspar M. Schwiedrzik cschwie...@mail.rockefeller.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, November 4, 2014 at 7:17 AM To: Freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Quality of surface-based alignment Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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] Fsaverage for ROI analysis of children
Hi Doug, Just wondering if you saw my response to your questions. Haven't heard anything from anyone else yet about my questions. Thanks in advance. In case you didn't see my response it is below: I made the ROI on an individual subject basis, not from fsaverage. Not sure if the labels I made came from the .aparc.annot files, what is the default of mri_annotation2label? I used the -outdir flag. Best, Michael S. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: Monday, November 03, 2014 9:32 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Fsaverage for ROI analysis of children Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I've noticed the ROI when registered to the fsaverage template is not in the correct position. I'm guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 Best, Michael S. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] Quality of surface-based alignment
Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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] Before recon-all, is it necessary to set origin of the image?
yes, that's fine On Tue, 4 Nov 2014, CHONNIKAN JONGKREANGKRAI wrote: Dear Bruce, Thank you for quick answer. I can use .nii file instead of dicom, right? Best Regards, Ngoak On 4 พ.ย. 2557, at 22:06, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Ngoaka no, you don't need to set the origin of the image. Just point recon-all at a single slice from the correct dicom series (of a highres T1-weighted scan) with the -i full path and file name of dicom slice -all -s subject id that you pick and you should be good to go cheers Bruce On Tue, 4 Nov 2014, CHONNIKAN JONGKREANGKRAI wrote: Dear all, I'm new on FreeSurfer. I want to calculate cortical thickness, hippocampus volume from MRI images (obtained from ADNI). After installation, I tried recon-all. Only this process, can I obtain cortical thickness and hippocampus volume? And someone told me that I have to set origin of the image of each case using SPM program. I want to know that is it necessary? Thank you for your kind attention Best Regards, Ngoak ___ 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.
Re: [Freesurfer] prefrontal cortex label
I don't know. Maybe someone else can weigh in. doug On 11/04/2014 07:38 AM, Anna Jonsson wrote: thank you. which labels are normally included as prefrontal cortex for freesurfer purposes? On Thu, Oct 23, 2014 at 5:04 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: You can use mri_annotation2label to break up the annotation into individual labels, then use mris_label2annot to recombine selected labels into an annotation or use mri_merge_label to merge them into a single label. All you have to do is decide with labels define prefontal doug On 10/23/2014 10:25 AM, Anna Jonsson wrote: Dear group, Is there a way to create a prefrontal cortex label in fresurfer? if so, please tell me the exact steps to do so, I am very confused. Thank you, Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 tel:617-724-2358 Fax: 617-726-7422 tel:617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Quality of surface-based alignment
Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe an output file that has something numerical on how much one surface had to be transformed to be aligned to the other. I could alternatively compute the square difference between the two surfaces, or something like that. Thanks! Caspar 2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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] Quality of surface-based alignment
You can look at how well the curvature and/or sulcal maps from your template overlay on the individual. doug On 11/04/2014 11:46 AM, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe an output file that has something numerical on how much one surface had to be transformed to be aligned to the other. I could alternatively compute the square difference between the two surfaces, or something like that. Thanks! Caspar 2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu: Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Quality of surface-based alignment
oh, I see. I would paint the folding patterns on the sphere.reg and toggle back and forth between them to see if they look right. Alternatively you could draw some sulci onto one of your datasets (this is easy to do in tksurfer) and use mri_label2label to map it to others and see if they land in the right place (central sulcus, calcarine, sylvian, etc...) On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe an output file that has something numerical on how much one surface had to be transformed to be aligned to the other. I could alternatively compute the square difference between the two surfaces, or something like that. Thanks! Caspar 2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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
Re: [Freesurfer] Fsaverage for ROI analysis of children
In that case, can you just use the mean thickness values as listed in subject/stats/?h.aparc.stats ? On 11/04/2014 10:33 AM, Smith, Michael wrote: Hi Doug, Just wondering if you saw my response to your questions. Haven’t heard anything from anyone else yet about my questions. Thanks in advance. In case you didn’t see my response it is below: I made the ROI on an individual subject basis, not from fsaverage. Not sure if the labels I made came from the .aparc.annot files, what is the default of mri_annotation2label? I used the -outdir flag. Best, Michael S. *From:*freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas Greve *Sent:* Monday, November 03, 2014 9:32 AM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Fsaverage for ROI analysis of children Can you back up and tell us what it is you are trying to do? Where did the ROI come from and how did you create it? doug On 11/3/14 8:56 AM, Smith, Michael wrote: Hello all, I have been conducting an ROI analysis and following the cortical thickness ROI tutorial found here: https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness. After going through this tutorial with a few of my subjects I’ve noticed the ROI when registered to the fsaverage template is not in the correct position. I’m guessing this is due to the nature of my subjects (children ranging from 8months-11 years old). Is there a better template I should use for this analysis? Also, when I run mri_segstats to get the cortical thickness for my ROI, will these numbers be inaccurate too? Thanks in advance! It is worth noting I am running Darwin-lion-stable-pub-v5.3.0 Best, Michael S. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Quality of surface-based alignment
Thanks! But there is nothing like a number I could pull from the registration process, e.g. the distances of the vertices in registration space? Caspar 2014-11-04 11:51 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: oh, I see. I would paint the folding patterns on the sphere.reg and toggle back and forth between them to see if they look right. Alternatively you could draw some sulci onto one of your datasets (this is easy to do in tksurfer) and use mri_label2label to map it to others and see if they land in the right place (central sulcus, calcarine, sylvian, etc...) On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Bruce and Matt, I should specify that I am working with non-human primate data, so unfortunately, looking at the parcellations would not work. I am aligning individuals to a a custom template that I made. I was wondering whether there is maybe an output file that has something numerical on how much one surface had to be transformed to be aligned to the other. I could alternatively compute the square difference between the two surfaces, or something like that. Thanks! Caspar 2014-11-04 11:19 GMT-05:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi Caspar the easiest way it so look at the parcellations and see if they are accurate. Note that we do subject-to-atlas alignment, not subject-to-subject (you get the latter by composing two atlas transforms) cheers Bruce On Tue, 4 Nov 2014, Caspar M. Schwiedrzik wrote: Hi Freesurfers, I was wondering whether there is a good way to assess post-hoc how well the alignment between two surfaces was. I wouldn't like to run the alignment again, but I could, if necessary. I would like to compare this alignment to a bunch of other alignments to see whether it was worse than the others. Thanks, Caspar ___ 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] mri_label2label
Dear all, I would like to draw a ROI on a group average surface (template) and map it back to the surface of individual subjects. For this, I would like to create the template based on my subjects, rather than using fsaverage. As far as I understood, I should first create the template by using: make_average_subject –out myAvg –subjects s1 s2 … Then, I should register each subject to the template with: mris_register --curv s1/surf/lh.sphere SUBJECTS_DIR/myAvg/lh.reg.template.tif s1/surf/lh.sphere.reg.myAvg. At this point, I can map the ROI to a given subject by using the command mri_label2label: mri_label2label --srclabel labelName --srcsubject myAvg --trgsubject s1 trglabel OutputLabelName --hemi lh --regmethod surface. There is one thing I don’t understand: how can I tell the command mri_label2label that it should use the registration file that I have created in the previous step (namely lh.sphere.reg.myAvg)? If I don't specify anything, is the function going to use the sphere.reg file that refers to the registration between subject s1 and fsaverage? In general, is the pipeline I described correct? Thanks a lot for your help. Best Roberta ___ 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_watershed -brain_atlas undocumented?
- This is a repost. It seems it did not come trough yesterday. Apologies if this becomes a double post - Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option -brain_atlas in the routine mri_watershed. However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for -atlas? Does the -brain_atlas flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 $ mri_watershed --version stable5 ___ 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_label2label
use --trgsurfreg sphere.reg.myAvg On 11/04/2014 12:27 PM, Roberta Santoro wrote: Dear all, I would like to draw a ROI on a group average surface (template) and map it back to the surface of individual subjects. For this, I would like to create the template based on my subjects, rather than using fsaverage. As far as I understood, I should first create the template by using: make_average_subject –out myAvg –subjects s1 s2 … Then, I should register each subject to the template with: mris_register --curv s1/surf/lh.sphere SUBJECTS_DIR/myAvg/lh.reg.template.tif s1/surf/lh.sphere.reg.myAvg. At this point, I can map the ROI to a given subject by using the command mri_label2label: mri_label2label --srclabel labelName --srcsubject myAvg --trgsubject s1 trglabel OutputLabelName --hemi lh --regmethod surface. There is one thing I don’t understand: how can I tell the command mri_label2label that it should use the registration file that I have created in the previous step (namely lh.sphere.reg.myAvg)? If I don't specify anything, is the function going to use the sphere.reg file that refers to the registration between subject s1 and fsaverage? In general, is the pipeline I described correct? Thanks a lot for your help. Best Roberta ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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_watershed -brain_atlas undocumented?
Hi Tom I'll cc Flo who wrote this code (a long time ago!). I think the -brain_atlas flag takes a gca atlas and uses it to avoid large-scale errors, while -atlas uses some built-in statistics about the shape and size of e.g. the cerebellum to avoid erasing it accidentally. Flo can correct me if I'm wrong :) cheers Bruce On Tue, 4 Nov 2014, tvg[fs] wrote: - This is a repost. It seems it did not come trough yesterday. Apologies if this becomes a double post - Hi all, I noticed that during skull stripping the standard recon-all pipeline uses option -brain_atlas in the routine mri_watershed. However documentation of this argument cannot be found in the help section or on the website. mri_watershed --help | less -p atlas https://surfer.nmr.mgh.harvard.edu/fswiki/mri_watershed?highlight=(atlas) Is this an undocumented flag or simply a synonym for -atlas? Does the -brain_atlas flag take an extra argument to specify the atlas? Thanks, Tom Specs: Mac OS X 10.8.5 freesurfer-Darwin-lion-stable-pub-v5.3.0 $ mri_watershed --version stable5 ___ 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] Create surface Labels of equal size
Dear Freesurfers, I would like to mark the brain surface (fsaverage) for an illustration of stimulation areas (TMS). I have calculated coordinates in Vertex RAS and Vertex Talairach. They are correctly located on the fsaverage surface in tksurfer. Is there a way to create labels of equal sizes at those coordinates? Ideally by using a script (since I have to mark them in 50 patients). this is purely for illustrative purposes. All coordinates are in fasaverage space. Any help would be appreciated, Bastian ___ 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] Create surface Labels of equal size
Hi Bastian you should be able to do this with a tcl script in tksurfer. Take a look at the ones we distribute for some examples cheers Bruce On Tue, 4 Nov 2014, Bastian Cheng wrote: Dear Freesurfers, I would like to mark the brain surface (fsaverage) for an illustration of stimulation areas (TMS). I have calculated coordinates in Vertex RAS and Vertex Talairach. They are correctly located on the fsaverage surface in tksurfer. Is there a way to create labels of equal sizes at those coordinates? Ideally by using a script (since I have to mark them in 50 patients). this is purely for illustrative purposes. All coordinates are in fasaverage space. Any help would be appreciated, Bastian ___ 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] Create surface Labels of equal size
Hi Bruce, thank you! I looked up all commands here: http://freesurfer.net/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference I guess what I should do is 1) mark vertex at coordinate 2) create label at marked vertex 3) maybe dilate the label. does this sound right? On 4 November 2014 23:24, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Bastian you should be able to do this with a tcl script in tksurfer. Take a look at the ones we distribute for some examples cheers Bruce On Tue, 4 Nov 2014, Bastian Cheng wrote: Dear Freesurfers, I would like to mark the brain surface (fsaverage) for an illustration of stimulation areas (TMS). I have calculated coordinates in Vertex RAS and Vertex Talairach. They are correctly located on the fsaverage surface in tksurfer. Is there a way to create labels of equal sizes at those coordinates? Ideally by using a script (since I have to mark them in 50 patients). this is purely for illustrative purposes. All coordinates are in fasaverage space. Any help would be appreciated, Bastian ___ 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
Re: [Freesurfer] Create surface Labels of equal size
yes, exactly On Tue, 4 Nov 2014, Bastian Cheng wrote: Hi Bruce, thank you! I looked up all commands here: http://freesurfer.net/fswiki/TkSurferGuide/TkSurferScripting/TkSurferScriptingReference I guess what I should do is 1) mark vertex at coordinate 2) create label at marked vertex 3) maybe dilate the label. does this sound right? On 4 November 2014 23:24, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Bastian you should be able to do this with a tcl script in tksurfer. Take a look at the ones we distribute for some examples cheers Bruce On Tue, 4 Nov 2014, Bastian Cheng wrote: Dear Freesurfers, I would like to mark the brain surface (fsaverage) for an illustration of stimulation areas (TMS). I have calculated coordinates in Vertex RAS and Vertex Talairach. They are correctly located on the fsaverage surface in tksurfer. Is there a way to create labels of equal sizes at those coordinates? Ideally by using a script (since I have to mark them in 50 patients). this is purely for illustrative purposes. All coordinates are in fasaverage space. Any help would be appreciated, Bastian ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Tracula_critical issue
Hi Anastasia, I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki. The problem is that when I am repeating the third step (trac-all -path -c ) for the same subjects to generate the statistics; Tracula is updating all the information mentioned in the file pathstats.overal.txt regarding the tract's volume and the tract's metrics values. Every time the output is different. I think we have a problem in the scripts or something like this? Attached are three pathstats.overal.txt files for the same subject after three consecutive runs for the trac-all -path -c (the same subject) Looking forward for your support Thanks # Title Pathway Statistics # # generating_program /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats --intrc /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr --dtbase /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dmri/dtifit --path fmajor --subj 002201 --out /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt --outvox /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname icepuff2 # machine x86_64 # user malshikh # anatomy_type pathway # # subjectname 002201 # pathwayname fmajor # Count 1500 Volume 1151 Len_Min 54 Len_Max 91 Len_Avg 71.1467 Len_Center 70 AD_Avg 0.00143148 AD_Avg_Weight 0.00148653 AD_Avg_Center 0.00146087 RD_Avg 0.000475763 RD_Avg_Weight 0.000414811 RD_Avg_Center 0.000390255 MD_Avg 0.000794336 MD_Avg_Weight 0.000772051 MD_Avg_Center 0.000747128 FA_Avg 0.593211 FA_Avg_Weight 0.653136 FA_Avg_Center 0.664371 # Title Pathway Statistics # # generating_program /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats --intrc /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr --dtbase /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dmri/dtifit --path fmajor --subj 002201 --out /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt --outvox /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname icepuff2 # machine x86_64 # user malshikh # anatomy_type pathway # # subjectname 002201 # pathwayname fmajor # Count 1500 Volume 998 Len_Min 55 Len_Max 105 Len_Avg 70.452 Len_Center 70 AD_Avg 0.00144797 AD_Avg_Weight 0.00148739 AD_Avg_Center 0.00147972 RD_Avg 0.000450739 RD_Avg_Weight 0.000414348 RD_Avg_Center 0.000411816 MD_Avg 0.00078315 MD_Avg_Weight 0.000772027 MD_Avg_Center 0.000767783 FA_Avg 0.614367 FA_Avg_Weight 0.654019 FA_Avg_Center 0.648396 # Title Pathway Statistics # # generating_program /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats # cvs_version # cmdline /usr/local/freesurfer/stable5_3_0/bin/dmri_pathstats --intrc /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr --dtbase /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dmri/dtifit --path fmajor --subj 002201 --out /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.overall.txt --outvox /autofs/cluster/transcend/malshikho/tractography/tracula_1/002201/dpath/fmajor_PP_avg33_mni_bbr/pathstats.byvoxel.txt # sysname Linux # hostname icepuff2 # machine x86_64 # user malshikh # anatomy_type pathway # # subjectname 002201 # pathwayname fmajor # Count 1500 Volume 693 Len_Min 56 Len_Max 97 Len_Avg 72.1413 Len_Center 29 AD_Avg 0.00150666 AD_Avg_Weight 0.00151482 AD_Avg_Center 0.00130182 RD_Avg 0.000431594 RD_Avg_Weight 0.000428958 RD_Avg_Center 0.000632432 MD_Avg 0.000789951 MD_Avg_Weight 0.000790911 MD_Avg_Center 0.000855561 FA_Avg 0.648118 FA_Avg_Weight 0.653595 FA_Avg_Center 0.457097 ___ 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] freeview fault: PETSC Error ...
you can try downloading our nightly 'dev' build of freeview, from here: https://surfer.nmr.mgh.harvard.edu/fswiki/Download or here's a quicker way (this is a one-line command... wget file): wget ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/freeview.bin and copy it to $FREESURFER_HOME/bin then chmod a+x $FREESURFER_HOME/bin/freeview.bin N. On Tue, 2014-11-04 at 12:35 +, Krieger, Donald N. wrote: I recently downloaded and installed freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz . I had been running this version previously but had to reload everything due to a disk crash. recon-all –all goes to completion with no errors. freeview starts up fine but fails on loading a volume file with the PETC error listed below. I found several references to this error in the archive but no resolution for my problem. Any thoughts would be welcome – thanks. [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: Unknown Name on a linux-gnu named BTRC-Server01 by kriegerd Tue Nov 4 06:55:17 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Regards, Don Signature0001 Don Krieger, Ph.D. Department of Neurological Surgery University ofPittsburgh (412)648-9654 Office (412)521-4431 Cell/Text ___ 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.
