[Freesurfer] mean cortical thickness on N ROIs
Dear FreeSurfers, suppose I should estimate the mean cortical thickness on a number N of ROIs (for instance, the left inferior temporal, the left middletemporal, and the left superior temporal). How would you suggest me to proceed? - Just performing a simple average of the 3 cortical thickness values obtained with the aparcstats2table? - Computing a weighted average of the 3 cortical thickness values obtained with the aparcstats2table? In this case, what would you use as weight? The area of the 3 regions? Thank you. Best, Elisa -- Elisa Veronese - PhD *Research Unit on Brain Imaging and Neuropsychology (RUBIN)* *Inter-University Center for Behavioral Neurosciences (ICBN)University of Udine and University of Verona, ItalyICBN Website: http://icbn.uniud.it/tiki-index.php http://icbn.uniud.it/tiki-index.php* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tracula update link not working
Hi, I apologise if this is only on my end but I can't seem to download any of the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful last week so I wonder if something's changed? Thanks Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com ___ 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] Fwd: mpr2mni305 failed error
Hi all! Sorry for my late answer but I went on holiday and I didn't have access to my mail. The background is normal in original dicoms and it is not an avarage of more than one run. The problem I reported was solved in all cases converting dicoms to nifti with dcm2nii and using the oriented volume. I don't know why but it functioned Is there a bug in freesurfer using directly dicoms? Thank you all for attention and advice. Francesco 2014-08-08 19:53 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: can you tar and gzip the dicoms and send them to us? Is there a high background level in them as well? Is this the average of more than one run? You should check the mri/orig/00?.mgz volume(s) as well On Fri, 8 Aug 2014, Francesco Deleo wrote: -- Forwarded message -- From: Francesco Deleo franc.de...@gmail.com Date: 2014-08-08 18:06 GMT+02:00 Subject: Re: [Freesurfer] mpr2mni305 failed error To: freesurfer freesurfer@nmr.mgh.harvard.edu It is not ok... It seems to have a contrast problem... I can send a snapshot, or if you want I can send the rawavg.mgz Francesco 2014-08-08 17:53 GMT+02:00 Bruce Fischl fis...@nmr.mgh.harvard.edu: what does the rawavg.mgz look like? If it is ok, can you email it to us? On Fri, 8 Aug 2014, Francesco Deleo wrote: Thank you all for attention and help! Maybe we're finding the problem: in cases I received the mpr2mni305 error the orig.mgz is unintelligible (it is white with some black point). But my dicoms are ok (I've checked!). I've already tried converting dicom to tiff but I got the same error message and the same unintelligible orig.mgz (and the tiff are ok too!). So I think the likely problem is in the recon-all -i command! Any idea? It remains a mistery for me why I have this problem only in some (and not in every one) MRI scans even if all the parameters are the same. thanks again Francesco 2014-08-07 17:16 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu: Have you looked in transforms/talairach_avi.log? On 08/07/2014 07:57 AM, Francesco Deleo wrote: Thank you Doug! but i tried it in many cases but I've always received the same error message... Is there something else I can try? Francesco 2014-08-07 0:46 GMT+02:00 Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu: Try it with -notal-check doug On 08/06/2014 04:39 PM, Francesco Deleo wrote: I all! I am a new freesurfer user. I have a problem when I perform the recon-all -all, in about 15% of MRI scans, all made with the same scanning protocol (T1 MPRAGE in a SIEMENS Avanto 1,5 T). I can't recognize any difference between those scans which work correctly and those not. I have never found the same error on 3T MRI scans. I've already tried to add these flags to the recon-all -all command: -use-mritotal -talairach -use-mritotal -notalairach but I've always received an error message Thank you very much ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin pro-di-villani.besta.local 13.3.0 Darwin Kernel Version 13.3.0: Tue Jun 3 21:27:35 PDT 2014; root:xnu-2422.110.17~1/RELEASE_X86_64 x86_64 Thanks very much for your attention Francesco Milan, Italy - FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Kernel info: Darwin 13.3.0 x86_64
[Freesurfer] labelled tissue segmentation mask back to native
Hello, I was wondering if FS has an output mask (labelled volume) for each tissue types (gm+wm+venctricular_csf) that I can then turn into each subject's native space. I understand I can use aseg.mgz or even aparc+aseg.mgz and then run mri_label2vol. But then how do I get correspondent labelling for each subject in it's own native space? Thanks, Alejandra ___ 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] tracula update link not working
Hi Kirstie - This was a glitch related to yesterday's storage cluster maintence. It's been fixed now, so please try again. a.y On Wed, 20 Aug 2014, Kirstie Whitaker wrote: Hi, I apologise if this is only on my end but I can't seem to download any of the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful last week so I wonder if something's changed? Thanks Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com ___ 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] tracula update link not working
Yep! Working now - thank you very much :) Kx On 20 August 2014 12:23, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Kirstie - This was a glitch related to yesterday's storage cluster maintence. It's been fixed now, so please try again. a.y On Wed, 20 Aug 2014, Kirstie Whitaker wrote: Hi, I apologise if this is only on my end but I can't seem to download any of the updates from http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. I was successful last week so I wonder if something's changed? Thanks Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com ___ 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. -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com ___ 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] tkmedit
Dear Don, Thanks alot for the attachment. I have installed it as recommended and tried the following and I started to get the error message below imaging@imaging-ThinkCentre-20:~$ freeview bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter: Permission denied When using sudo before the above command and entering the password i get the following message: imaging@imaging-ThinkCentre-20:~$ sudo tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz sudo: tkmedit: command not found Any idea??? On Tue, Aug 19, 2014 at 4:26 PM, Krieger, Donald N. krieg...@upmc.edu wrote: Hi Ali, You are missing the tcsh interpreter. It should be located at /bin/tcsh typically. It usually comes with the operating system but may not have been installed or may be in the wrong place for freesurfer to find it. I’ve attached a 64 bit i86 version which is from my installation of Fedora Linus. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text *From:* freesurfer-boun...@nmr.mgh.harvard.edu [mailto: freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Ali Radaideh *Sent:* Tuesday, August 19, 2014 8:06 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] tkmedit Thanks ZK, I got the following message: bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: No such file or directory On Tue, Aug 12, 2014 at 5:29 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Ali, I have not encountered this issue before. Could you please provide a screencapture or copy/paste of the terminal output when you type: $ tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz -Zeke On 08/12/2014 06:48 AM, Ali Radaideh wrote: Dear Zeke, Thanks for your email. For some reasons your email went to the spam folder The build-stamps.txt file contents: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 freeview does not work Thanks, Ali On Tue, Aug 5, 2014 at 11:44 PM, Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu wrote: Just so its clear.. You have installed FreeSurfer on 15 Linux machines running Ubuntu? If so, can you please provide me with the contents of the build-stamps.txt file in the FREESURFER_HOME directory? Also, could you please inform me if freeview works by simply typing the freeview command? $ freeview -Zeke On 08/05/2014 04:32 PM, Ali Radaideh wrote: Dear FreeSurfer experts, I have installed FreeSurfer on multiple machines in our image processing lab (15 PC, Linux Ubuntu) and made sure that the setting are fine. However, I have tried to test if freesurfer works or not by typing the following: tkmedit bert orig.mgz Unfortunately, I have got the following error message on all PCs A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. So what would be the error? Many thanks in advance, Ali, -- /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 / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ 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 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. -- /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
[Freesurfer] Some notes on getting Tracula to work for newbies
Hi Anastasia and the freesurfer list, I've been working on getting the latest version of tracula to run and I thought I would post here the errors that I've worked around. It's all been based on looking through the mailing list archives but I thought it would be useful to add them here all in one place! The goal of this email is simply to save time for others in the future (including myself when I forget all these things!) [Note that if I've written something between then it will be specific to your files/directories etc] When running trac-all on an input nii file with corresponding bval and bvec files: 1) If you're getting an error that says: nifti1Read(): unsupported slice timing pattern 5 in NAME OF YOUR DTI NIFTI FILE Try running the command: fslmaths NAME OF YOUR DTI NIFTI FILE NAME OF YOUR DTI NIFTI FILE eg: fslmaths dti.nii.gz dti.nii.gz I'm really not clear on what exactly is wrong with my files (created using an in house dicom converter) but taking in the file and writing it straight back out again gets rid of this problem for me. 2) If you're getting an error that says ERROR: Could not open SUBJECTS_DIR/SUBID/dmri/bvals for reading Then you're probably using the centos4 update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options - if the centos6 update works then switch to that, otherwise all other steps in trac-all -prep work *except* for the quality control. So you can run trac-all -prep -noqa and all should be well. To install the update just download it (I used wget TRACULA_UPDATE_LINK) and the untar it (tar -zxvf TRACULA_UPDATE_TAR.GZ_FILE). Copy the files inside the folder you've created into the $FREESURFER_HOME/bin/ directory. 3) If you're getting an error that says (something along the lines of) mri_convert --frame 0 14 27 41 54 68 SUBJECTS_DIR/SUBID/dmri/dwi.nii.gz SUBJECTS_DIR/SUBID/dmri/lowb.nii.gz mri_convert: extra arguments (41 and following) type mri_convert -u for usage Then you're probably using an old version of trac-all. Double check that you've replaced the appropriate files in your $FREESURFER_HOME/bin directory with those contained in the appropriate update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. (See my instructions at point 2). Some fun facts from my experience: You can have decimal points (not commas though) in your bvals files. You can run trac-all in either a bash or tcsh shell. (These were not the droids I was looking for) Thanks again for the really excellent software. And please correct anything that I've written here if it's wrong! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com ___ 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] Some notes on getting Tracula to work for newbies
Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You are a model user :) On Wed, 20 Aug 2014, Kirstie Whitaker wrote: Hi Anastasia and the freesurfer list, I've been working on getting the latest version of tracula to run and I thought I would post here the errors that I've worked around. It's all been based on looking through the mailing list archives but I thought it would be useful to add them here all in one place! The goal of this email is simply to save time for others in the future (including myself when I forget all these things!) [Note that if I've written something between then it will be specific to your files/directories etc] When running trac-all on an input nii file with corresponding bval and bvec files: 1) If you're getting an error that says: nifti1Read(): unsupported slice timing pattern 5 in NAME OF YOUR DTI NIFTI FILE Try running the command: fslmaths NAME OF YOUR DTI NIFTI FILE NAME OF YOUR DTI NIFTI FILE eg: fslmaths dti.nii.gz dti.nii.gz I'm really not clear on what exactly is wrong with my files (created using an in house dicom converter) but taking in the file and writing it straight back out again gets rid of this problem for me. 2) If you're getting an error that says ERROR: Could not open SUBJECTS_DIR/SUBID/dmri/bvals for reading Then you're probably using the centos4 update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options - if the centos6 update works then switch to that, otherwise all other steps in trac-all -prep work *except* for the quality control. So you can run trac-all -prep -noqa and all should be well. To install the update just download it (I used wget TRACULA_UPDATE_LINK) and the untar it (tar -zxvf TRACULA_UPDATE_TAR.GZ_FILE). Copy the files inside the folder you've created into the $FREESURFER_HOME/bin/ directory. 3) If you're getting an error that says (something along the lines of) mri_convert --frame 0 14 27 41 54 68 SUBJECTS_DIR/SUBID/dmri/dwi.nii.gz SUBJECTS_DIR/SUBID/dmri/lowb.nii.gz mri_convert: extra arguments (41 and following) type mri_convert -u for usage Then you're probably using an old version of trac-all. Double check that you've replaced the appropriate files in your $FREESURFER_HOME/bin directory with those contained in the appropriate update at http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. (See my instructions at point 2). Some fun facts from my experience: * You can have decimal points (not commas though) in your bvals files. * You can run trac-all in either a bash or tcsh shell. (These were not the droids I was looking for) Thanks again for the really excellent software. And please correct anything that I've written here if it's wrong! Kx -- Kirstie Whitaker, PhD Research Associate Department of Psychiatry University of Cambridge Mailing Address Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB Phone: +44 7583 535 307 Website: www.kirstiewhitaker.com ___ 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] Creating the FSDG file for more than one discrete variable
Dear Freesurfer gurus, I am trying to create an FSDG file for my data set and I have a question regarding discrete variables. So say this is my data: Two discrete variables (two with two levels, one with eight), one continuous variable. I'm interested in one discrete variable (Patient/Control) with two levels and want to account for the effect of the others in the analysis. How should I construct my FSDG file? Can I have three columns for discrete variables (1) or should I have one column (2)? Or is there another way? (1) So should I do: GroupDescriptorFile 1 Title GroupAnalysis Class Male Class Female Class Patient Class Control Class ImagingsiteOne Class ImagingsiteTwo [and so on...] Class OccupationEight VariablesAge Subject1MalePatientImagingsiteThree16 Subject2MaleControlImagingsiteSeven18 Subject3FemalePatientImagingsiteThree23 And so on OR (2) Should I do GroupDescriptorFile 1 Title GroupAnalysis Class MalePatientImagingsiteOne Class MalePatient?ImagingsiteTwo [and so on..] Class MalePatient?ImagingsiteEight Class MaleControlImagingsiteOne [and so on...] Class FemalePatient?ImagingsiteOne [and so on until...] Class FemaleControl?ImagingsiteEight VariablesAge Subject1MalePatientImagingsiteThree16 Subject2MaleControlImagingsiteSeven18 Subject3FemalePatientImagingsiteThree?23 And so on Thank you! Best wishes, Hanna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] FreeSurfer platform/performance questions
Thanks for the reply Zeke. I understand what you are saying about the VM. So my question is now, how do we help our users to optimize FreeSurfer for their large scale data sets? We have a couple of Red Hat Enterprise Linux 6 64bit machines with the newest FreeSurfer installed (freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz), and these machines are very powerful. (16 x 3.3GHz cores, 128GB of memory, 1888 Bus speed, Nvidia Quadro K5000 video, etc.) We have encouraged our users to use these machines, but they have hesitated because I think a lot of their data has already been processed on the XUbuntu VM and they are worried about switching the FreeSurfer platforms in the middle of their research. I wonder if it makes sense for them to restart their entire processing run on the RHEL6 machines. If the processing is that much faster, then they may save time in the long run? But then our users have also requested a fresh Ubuntu install with FreeSurfer installed on top? (not a VM) Is there anything about Ubutnu OS that is better suited for FreeSurfer than Red Hat Enterprise 6 or 7? Alex -Original Message- From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] Sent: Tuesday, August 19, 2014 4:28 PM To: Freesurfer support list; Lazarevich, Alexander Subject: Re: [Freesurfer] FreeSurfer platform/performance questions Hello Alex, I created the FreeSurfer VM and you are correct that the Virtual Box host is 32bit. I cant remember exactly why I did it that way, but I suspect it may have been in an effort to reduce overall size, as the gzipped size of the .vdi file is 9gigs. Also, it was created more as matter of convenience to allow users with PCs the means for viewing and processing data, but it is not optimized for processing large scale data sets. There is no 64bit VM currently available. However, it would not be too difficult to make one. Simply download any of the available 64bit host images (http://virtualboxes.org/images/), open it in VirtualBox, install 64bit freesurfer within the image, and then export the disk image which will now have freesurfer installed on it. I could take on this task but I can not guarantee I will get to it in the immediate future. -Zeke On 08/18/2014 12:07 PM, Lazarevich, Alexander wrote: One of the packages we have recently installed upon request is FreeSurfer. We have installed freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer -Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz on our Red Hat Enterprise Linux 6 workstations, as well as on our Windows 7 Enterprise 64bit workstations. We have also installed Oracle's VirtualBox on a Windows 7 Enterprise 64bit machine, and run the VM freesurfer-Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer -Virtualbox-linux-x86-stable-pub-v5.3-full.vdi.gz inside that virtual environment. The researchers who requested FreeSurfer are all part of the same group, and they are trying to complete a very large research project which requires FreeSurfer to process large amounts of data. They have normally been running FreeSurfer on the VM in the XUbuntu VirtualBox environment on their own average desktop PC's. However, they are concerned about their processing time with FreeSurfer, so they are hoping to take advantage of the Vislab computing resources to decrease the processing time in FreeSurfer. We are running into the following problems/concerns: 1)The FreeSurfer VM (Xubuntu) that runs in VirtualBox is a 32bit host. Is there a 64bit VM available? That 32bit host can only access 4GB of memory, whereas they would like to be able to access more of the workstations 128GB of memory. 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] Open MP parallel processing scaling factor?
Hello all, Traditionally I have only processed FS data using a single core per person, but processing many people at once. Now we have caught up with the backlog of scans, we have a continuos trickle of scans coming in 1 by 1. I was wondering if anyone has tested how the speed-up of open-mp varies with number of cores used simultaneously. For example how much faster is using 100 cores versus 10? I am trying to find a sweet spot of resource usage and speed. Thanks! -Andrew ___ 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] Creating the FSDG file for more than one discrete variable
Hi Hanna, use #2 doug On 08/20/2014 10:36 AM, Isotalus, Hanna wrote: Dear Freesurfer gurus, I am trying to create an FSDG file for my data set and I have a question regarding discrete variables. So say this is my data: Two discrete variables (two with two levels, one with eight), one continuous variable. I'm interested in one discrete variable (Patient/Control) with two levels and want to account for the effect of the others in the analysis. How should I construct my FSDG file? Can I have three columns for discrete variables (1) or should I have one column (2)? Or is there another way? (1) So should I do: GroupDescriptorFile 1 Title GroupAnalysis Class Male Class Female Class Patient Class Control Class ImagingsiteOne Class ImagingsiteTwo [and so on...] Class OccupationEight Variables Age Subject1 Male Patient ImagingsiteThree 16 Subject2 Male Control ImagingsiteSeven 18 Subject3 Female Patient ImagingsiteThree 23 And so on OR (2) Should I do GroupDescriptorFile 1 Title GroupAnalysis Class MalePatientImagingsiteOne Class MalePatientImagingsiteTwo [and so on..] Class MalePatientImagingsiteEight Class MaleControlImagingsiteOne [and so on...] Class FemalePatientImagingsiteOne [and so on until...] Class FemaleControlImagingsiteEight Variables Age Subject1 MalePatientImagingsiteThree 16 Subject2 MaleControlImagingsiteSeven 18 Subject3 FemalePatientImagingsiteThree 23 And so on Thank you! Best wishes, Hanna ___ 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] Custom aseg Color Lookup Table
Try loading aseg.mgz as the aux volume so you can see the number at a particular voxel. If the color is not correct, see what the number is and what it corresponds to in the LUT doug On 08/19/2014 05:57 PM, C.P. Frost wrote: Hi all, I'm trying to use Freeview to display subcortical regions in aseg.mgz with a custom color lookup table. RGB colors will indicate on a jet scheme how well that region's volume correlates to performance on a behavioral measure. In other words, an R^2 coefficient of -1 is dark blue, 0 is green, and 1 is dark red. I adapted the approach for aseg structures from this method: http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours/ When I try right now, by e.g. loading subjects_dir/average/mri/aseg.mgz, and choosing Color map Lookup Table, Lookup Table Load lookup table... and selecting my custom table file, it *almost* works. The file is copied below (it has no headers). 4 Left-Lateral-Ventricle 92 255 163 0 5 Left-Inf-Lat-Vent 224 255 31 0 7 Left-Cerebellum-White-Matter 112 255 143 0 8 Left-Cerebellum-Cortex 133 255 122 0 10 Left-Thalamus-Proper 153 255 102 0 11 Left-Caudate 102 255 153 0 12 Left-Putamen 61 255 194 0 13 Left-Pallidum 102 255 153 0 14 3rd-Ventricle 0 224 255 0 15 4th-Ventricle 61 255 194 0 16 Brain-Stem 71 255 184 0 17 Left-Hippocampus 102 255 153 0 18 Left-Amygdala 41 255 214 0 26 Left-Accumbens-area 92 255 163 0 28 Left-VentralDC 122 255 133 0 30 Left-vessel 102 255 153 0 31 Left-choroid-plexus 102 255 153 0 43 Right-Lateral-Ventricle 173 255 82 0 44 Right-Inf-Lat-Vent 122 255 133 0 41 Right-Cerebellum-White-Matter 82 255 173 0 42 Right-Cerebellum-Cortex 122 255 133 0 49 Right-Thalamus-Proper 173 255 82 0 50 Right-Caudate 143 255 112 0 51 Right-Putamen 92 255 163 0 52 Right-Pallidum 41 255 214 0 53 Right-Hippocampus 133 255 122 0 54 Right-Amygdala 20 255 235 0 58 Right-Accumbens-area 82 255 173 0 60 Right-VentralDC 122 255 133 0 62 Right-vessel 122 255 133 0 63 Right-choroid-plexus 143 255 112 0 72 5th-Ventricle 92 255 163 0 85 Optic-Chiasm 112 255 143 0 251 CC_Posterior 71 255 184 0 252 CC_Mid_Posterior 31 255 224 0 253 CC_Central 10 255 245 0 The index numbers were chosen to match those found in the default aseg LUT, as listed on the FS wiki: FSTutorial AnatomicalROI FreeSurferColorLUT. Some regions appear correctly, but others either a) display with incorrect labels, particularly Right-Cerebellum-White-Matter or Right-Cerebellum-Cortex on *cortical* white matter and ribbon, or b) display with no label in the info panel, which makes it unclear whether it's working. Notes: - Originally indices were simply 1 to n, but that caused a wider array of problems, and I inferred (perhaps incorrectly) freeview was matching regions with indices rather than label names. -This particular map is mostly green since most correlations are small, which is fine; others will have a broader range of values. -I'm not sure what the effect is of pressing the Show existing labels only toggle, which eliminates a couple areas from the label list, but it's unclear how it chooses them. Can anyone offer advice on how to ensure the correct colors are displayed in the correct regions? (Or an easier way to do this?) Cheers, C.P. Frost UW-Madison ___ 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] Open MP parallel processing scaling factor?
hi andrew, i haven't done many systematic comparisons but there are a few practical considerations to take into account. in recon-all, i believe a few steps are affected by the openmp option and that creates resource underutilization. processors run idle when those steps are not being run. in my ad hoc analysis i have found i can process a single subject in about 5 hours using openmp 8, but that holds up 8 processors for that subject. the same subject can be processed in about 12 hours one 1 processor. say i have 16 processors, i can process 16 subjects in say 12 hours using 1 processor per recon. however, using 8 per recon would take about 40 hours, 2 subjects every 5 hours. so on our cluster, we tend to process with openmp 1 or 2 depending on the average load on the cluster. this is also dependent on your hardware, amount of memory, cluster scheduler, etc.,. if i really need speed on an individual case i go with -openmp 8. cheers, satra On Wed, Aug 20, 2014 at 11:04 AM, O'Shea,Andrew aos...@ufl.edu wrote: Hello all, Traditionally I have only processed FS data using a single core per person, but processing many people at once. Now we have caught up with the backlog of scans, we have a continuos trickle of scans coming in 1 by 1. I was wondering if anyone has tested how the speed-up of open-mp varies with number of cores used simultaneously. For example how much faster is using 100 cores versus 10? I am trying to find a sweet spot of resource usage and speed. Thanks! -Andrew ___ 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] tkmedit
Hi Ali, Sorry it didn’t work “out of the box.” It was kind of a long shot. That interpreter is for an i86 64bit system running linux. If you are running a Mac or have a 32bit os or … it will be a problem. If it’s the right one, it needs to be enabled for execution with the following command: chmod –v 755 /bin/tcsh This is system administrator stuff which I’m sure others on the list know much better than me. I’m sure you can grab the correct version of tcsh for your OS from somewhere on the web. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ali Radaideh Sent: Wednesday, August 20, 2014 8:17 AM To: Freesurfer support list Subject: Re: [Freesurfer] tkmedit Dear Don, Thanks alot for the attachment. I have installed it as recommended and tried the following and I started to get the error message below imaging@imaging-ThinkCentre-20:~$ freeview bash: /usr/local/freesurfer/bin/freeview: /bin/tcsh: bad interpreter: Permission denied When using sudo before the above command and entering the password i get the following message: imaging@imaging-ThinkCentre-20:~$ sudo tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz sudo: tkmedit: command not found Any idea??? On Tue, Aug 19, 2014 at 4:26 PM, Krieger, Donald N. krieg...@upmc.edumailto:krieg...@upmc.edu wrote: Hi Ali, You are missing the tcsh interpreter. It should be located at /bin/tcsh typically. It usually comes with the operating system but may not have been installed or may be in the wrong place for freesurfer to find it. I’ve attached a 64 bit i86 version which is from my installation of Fedora Linus. Regards, Don Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edumailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ali Radaideh Sent: Tuesday, August 19, 2014 8:06 AM To: Freesurfer support list Subject: Re: [Freesurfer] tkmedit Thanks ZK, I got the following message: bash: /usr/local/freesurfer/bin/tkmedit: /bin/tcsh: bad interpreter: No such file or directory On Tue, Aug 12, 2014 at 5:29 PM, Z K zkauf...@nmr.mgh.harvard.edumailto:zkauf...@nmr.mgh.harvard.edu wrote: Ali, I have not encountered this issue before. Could you please provide a screencapture or copy/paste of the terminal output when you type: $ tkmedit -f $FREESURFER_HOME/subjects/sample-001.mgz -Zeke On 08/12/2014 06:48 AM, Ali Radaideh wrote: Dear Zeke, Thanks for your email. For some reasons your email went to the spam folder The build-stamps.txt file contents: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0 freeview does not work Thanks, Ali On Tue, Aug 5, 2014 at 11:44 PM, Z K zkauf...@nmr.mgh.harvard.edumailto:zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edumailto:zkauf...@nmr.mgh.harvard.edu wrote: Just so its clear.. You have installed FreeSurfer on 15 Linux machines running Ubuntu? If so, can you please provide me with the contents of the build-stamps.txt file in the FREESURFER_HOME directory? Also, could you please inform me if freeview works by simply typing the freeview command? $ freeview -Zeke On 08/05/2014 04:32 PM, Ali Radaideh wrote: Dear FreeSurfer experts, I have installed FreeSurfer on multiple machines in our image processing lab (15 PC, Linux Ubuntu) and made sure that the setting are fine. However, I have tried to test if freesurfer works or not by typing the following: tkmedit bert orig.mgz Unfortunately, I have got the following error message on all PCs A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. So what would be the error? Many thanks in advance, Ali, -- /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.jomailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jomailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jomailto:ali.radai...@hu.edu.jo mailto:ali.radai...@hu.edu.jomailto:ali.radai...@hu.edu.jo / /webpage: http://staff.hu.edu.jo/Default.aspx?id=ABZUPDzYeqM=/ ___ Freesurfer mailing list
[Freesurfer] problem downloading freesurfer
Hi I tried for three days download freesurfer even today but pressing the download link in http://surfer.nmr.mgh.harvard.edu/fswiki/Download These are fallen and message This web page is not available I have understood that the site was in maintenance, however the links do not even respond. any help? I need to download for Mac OS XV FreeSurfer 10.9.4 64bit regards -- *Gamaliel Huerta* *Ingeniería Civil Biomédica* *Universidad de Valparaíso* ___ 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] Some notes on getting Tracula to work for newbies
On 20 August 2014 14:27, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu
wrote:
Thanks a lot, Kirstie. Nice job on finding solutions in the archives! You
are a model user :)
Thank youalthough unfortunately not quite the best user - I still have
problems...
I think I lied in my earlier email - I think that the mri_convert problem
(#3 below) is actually in the newest version of trac-preproc. (I didn't do
a great job of keeping track of my version because I was being lazy! More
fool me.)
Here's the part of the code which in the May 2014 update ('$Id:
trac-preproc,v 1.49 2014/03/22 03:31:22 ayendiki Exp $' ) that is leading
to the error:
#=
# Make diffusion brain mask
if ($#nb0 0) then
set lowblist = ()
@ k = 0
while ($k $nb0)
set lowblist = ($lowblist $k)
@ k = $k + 1
end
else
set bmin = `grep -v ^$ $dwidir/dwi_orig.mghdti.bvals \
| sort --numeric-sort | head -1`
set lowblist = `cat $dwidir/dwi_orig.mghdti.bvals \
| awk -v bmin=$bmin '{if ($1 == bmin) print NR-1}'`
endif
if (! $#lowblist) then
echo ERROR: Cannot detect low-b volumes
goto error_exit
endif
set cmd = mri_convert
set cmd = ($cmd --frame $lowblist)
set cmd = ($cmd $dwidir/dwi.nii.gz)
set cmd = ($cmd $dwidir/lowb.nii.gz)
echo $cmd | tee -a $LF | tee -a $CF
if ($RunIt) then
$cmd | tee -a $LF
if ($status) goto error_exit
endif
#=
Which leads to this command:
mri_convert --frame 0 14 27 41 54 68
/scratch/kw401/UCHANGE_INTERIM/SUB_DATA/10778/SURFER/MRI0/dmri/dwi.nii.gz
/scratch/kw401/UCHANGE_INTERIM/SUB_DATA/10778/SURFER/MRI0/dmri/lowb.nii.gz
And then to this error:
mri_convert: extra arguments (41 and following)
I made the following changes to the code (trac-preproc) and everything
seems to run just fine.
#=
OLD
set cmd = ($cmd --frame $lowblist)
NEW
set cmd = ($cmd --frame ${lowblist[1]})
#=
What do you think? Is this just an odd-ness for me, or is it a helpful fix?
One thing that I haven't been able to ascertain is whether I have an old
version of mri_convert that should be able to concatenate the six listed
volumes! (The next section of code seems to look like its trying to
concatenate volumes so it might be expecting a 4D file? Or multiple
lowb.nii.gz volumes?)
I hope this all makes sense! Thank you again for all your hard work!
Kx
On Wed, 20 Aug 2014, Kirstie Whitaker wrote:
Hi Anastasia and the freesurfer list,
I've been working on getting the latest version of tracula to run and I
thought I would post here the errors that I've worked around. It's all been
based on looking
through the mailing list archives but I thought it would be useful to
add them here all in one place! The goal of this email is simply to save
time for others in the
future (including myself when I forget all these things!)
[Note that if I've written something between then it will be
specific to your files/directories etc]
When running trac-all on an input nii file with corresponding bval and
bvec files:
1) If you're getting an error that says:
nifti1Read(): unsupported slice timing pattern 5 in NAME OF YOUR DTI
NIFTI FILE
Try running the command:
fslmaths NAME OF YOUR DTI NIFTI FILE NAME OF YOUR DTI NIFTI FILE
eg: fslmaths dti.nii.gz dti.nii.gz
I'm really not clear on what exactly is wrong with my files (created
using an in house dicom converter) but taking in the file and writing it
straight back out again
gets rid of this problem for me.
2) If you're getting an error that says
ERROR: Could not open SUBJECTS_DIR/SUBID/dmri/bvals for reading
Then you're probably using the centos4 update at
http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula. You have two options -
if the centos6 update works then switch to
that, otherwise all other steps in trac-all -prep work *except* for the
quality control. So you can run trac-all -prep -noqa and all should be well.
To install the update just download it (I used wget
TRACULA_UPDATE_LINK) and the untar it (tar -zxvf
TRACULA_UPDATE_TAR.GZ_FILE). Copy the files inside the folder
you've created into the $FREESURFER_HOME/bin/ directory.
3) If you're getting an error that says (something along the lines of)
mri_convert --frame 0 14 27 41 54 68
SUBJECTS_DIR/SUBID/dmri/dwi.nii.gz
SUBJECTS_DIR/SUBID/dmri/lowb.nii.gz
mri_convert: extra arguments (41 and following)
type mri_convert -u for usage
Then you're probably using an old version of trac-all. Double check that
you've replaced the appropriate files in your $FREESURFER_HOME/bin
directory with those
contained in the appropriate update at
Re: [Freesurfer] problem downloading freesurfer
It appears to work for me. Try this link to download directly: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0/freesurfer-Darwin-lion-stable-pub-v5.3.0.dmg Once downloaded, go here for installation notes: http://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall This should work on OSX Mavericks (v 10.9). If you install and you get a segfault error when attempting to open any of the freesurfer GUIs then please reinstall XQuartz v2.7.5 (http://xquartz.macosforge.org/trac/wiki/Releases) Hope this helps! Best, Lee On Wed, 2014-08-20 at 12:57 -0400, gamaliel huerta urrea wrote: Hi I tried for three days download freesurfer even today but pressing the download link in http://surfer.nmr.mgh.harvard.edu/fswiki/Download These are fallen and message This web page is not available I have understood that the site was in maintenance, however the links do not even respond. any help? I need to download for Mac OS XV FreeSurfer 10.9.4 64bit regards -- Gamaliel Huerta Ingeniería Civil Biomédica Universidad de Valparaíso ___ 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] Creating lower resolution surface models
I am running analysis where I am taking fMRI data using Freesurfer to project it onto the cortical surface and load it into Brainstorm to use as a constraint on the source reconstruction. I am able to do all the steps just fine, the problem I am encountering is that Freesurfer creates a surface with 200,000+ vertices, for the analysis I am running I downsample it in brainstorm to 15,000 vertices to reduce run time. However, when the label file for Freesurfeer gets down sampled it significantly changes how the scouts look. Is there a way to have Freesurfer create a surface with 15000 vertices and then project the volumetric fMRI onto that surface so I don't have to downsample the data? I know there is the function fmris_decimate, which should allow me to decimate targeted files. But I am not sure if I can then use mdi_vol2surf to put the fMRI data onto the decimated surface files, or if I need to have the entire surface file generated from the beginning with only 15,000 vertices. Can I use the recon-all function to define the number of vertices I want, or is that a variable I can't adjust? Any help in the matter would be appreciated. Nicholas ___ 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_tessellate: max vertices 1000000 exceeded
Hello, The latest version of mri_tessellate can be downloaded using this the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate It would be wise to backup your existing version befor overwriting it with the version contained in the link above. -Zeke On 08/19/2014 05:52 PM, Michiel Kleinnijenhuis wrote: Hi, While doing a high resolution ex vivo recon job, I came across the error mri_tessellate: max vertices 100 exceeded As mentioned in the threads http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35305.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35305.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31331.html there seems to be an easy fix. Does anyone have a compiled version of mri_tesselate with the vertex limit relaxed; for Mac (freesurfer-Darwin-lion-stable-pub-v5.3.0)? Thanks! Michiel Kleinnijenhuis == *Michiel Kleinnijenhuis* Postdoctoral researcher FMRIB Centre Nuffield Department of Clinical Neurosciences University of Oxford ___ 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] Fwd: Re: Custom aseg Color Lookup Table
Thanks for the reply, Doug. The main problem is that areas not included in my custom table appear colored in freeview. These areas' numbers correctly correspond to their indices on the default FreeSurferColorLUT, although they don't appear labeled in the info panel, nor are they listed to the left of the main display. For instance, the left cerebral cortex (not on my list) is colored, and clicking on it yields an index of 3 in the info panel, but no label. The good news is so far as I can tell, every area I specified does show up colored appropriately and has a label associated, but I have no idea where the ones I DIDN'T specify are coming from. Original Message Subject:Re: [Freesurfer] Custom aseg Color Lookup Table Date: Wed, 20 Aug 2014 11:12:56 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Try loading aseg.mgz as the aux volume so you can see the number at a particular voxel. If the color is not correct, see what the number is and what it corresponds to in the LUT doug On 08/19/2014 05:57 PM, C.P. Frost wrote: Hi all, I'm trying to use Freeview to display subcortical regions in aseg.mgz with a custom color lookup table. RGB colors will indicate on a jet scheme how well that region's volume correlates to performance on a behavioral measure. In other words, an R^2 coefficient of -1 is dark blue, 0 is green, and 1 is dark red. I adapted the approach for aseg structures from this method: http://brainder.org/2011/07/05/freesurfer-brains-in-arbitrary-colours/ When I try right now, by e.g. loading subjects_dir/average/mri/aseg.mgz, and choosing Color map Lookup Table, Lookup Table Load lookup table... and selecting my custom table file, it *almost* works. The file is copied below (it has no headers). 4 Left-Lateral-Ventricle 92 255 163 0 5 Left-Inf-Lat-Vent 224 255 31 0 7 Left-Cerebellum-White-Matter 112 255 143 0 8 Left-Cerebellum-Cortex 133 255 122 0 10 Left-Thalamus-Proper 153 255 102 0 11 Left-Caudate 102 255 153 0 12 Left-Putamen 61 255 194 0 13 Left-Pallidum 102 255 153 0 14 3rd-Ventricle 0 224 255 0 15 4th-Ventricle 61 255 194 0 16 Brain-Stem 71 255 184 0 17 Left-Hippocampus 102 255 153 0 18 Left-Amygdala 41 255 214 0 26 Left-Accumbens-area 92 255 163 0 28 Left-VentralDC 122 255 133 0 30 Left-vessel 102 255 153 0 31 Left-choroid-plexus 102 255 153 0 43 Right-Lateral-Ventricle 173 255 82 0 44 Right-Inf-Lat-Vent 122 255 133 0 41 Right-Cerebellum-White-Matter 82 255 173 0 42 Right-Cerebellum-Cortex 122 255 133 0 49 Right-Thalamus-Proper 173 255 82 0 50 Right-Caudate 143 255 112 0 51 Right-Putamen 92 255 163 0 52 Right-Pallidum 41 255 214 0 53 Right-Hippocampus 133 255 122 0 54 Right-Amygdala 20 255 235 0 58 Right-Accumbens-area 82 255 173 0 60 Right-VentralDC 122 255 133 0 62 Right-vessel 122 255 133 0 63 Right-choroid-plexus 143 255 112 0 72 5th-Ventricle 92 255 163 0 85 Optic-Chiasm 112 255 143 0 251 CC_Posterior 71 255 184 0 252 CC_Mid_Posterior 31 255 224 0 253 CC_Central 10 255 245 0 The index numbers were chosen to match those found in the default aseg LUT, as listed on the FS wiki: FSTutorial AnatomicalROI FreeSurferColorLUT. Some regions appear correctly, but others either a) display with incorrect labels, particularly Right-Cerebellum-White-Matter or Right-Cerebellum-Cortex on *cortical* white matter and ribbon, or b) display with no label in the info panel, which makes it unclear whether it's working. Notes: - Originally indices were simply 1 to n, but that caused a wider array of problems, and I inferred (perhaps incorrectly) freeview was matching regions with indices rather than label names. -This particular map is mostly green since most correlations are small, which is fine; others will have a broader range of values. -I'm not sure what the effect is of pressing the Show existing labels only toggle, which eliminates a couple areas from the label list, but it's unclear how it chooses them. Can anyone offer advice on how to ensure the correct colors are displayed in the correct regions? (Or an easier way to do this?) Cheers, C.P. Frost UW-Madison ___ 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
Re: [Freesurfer] Open MP parallel processing scaling factor?
Andrew, I basically agree with everything Satra is saying. Just as an added piece if info, Ive included a chart which did a systematic study of recon-all processing times with different number of cpus in parallel. These results are a bit old (and might be for low-res data) but the general idea is that there is a point of diminishing returns after using 4 processors in parallel. The gain from using more processors may be worth it for you. There are other tricks to getting faster recons (like processing left and right hemishperes in parallel) but that is a bit more tricky and requires a custom script. I can provide additional information if you think you would like to pursue that avenue -Zeke On 08/20/2014 11:21 AM, Satrajit Ghosh wrote: hi andrew, i haven't done many systematic comparisons but there are a few practical considerations to take into account. in recon-all, i believe a few steps are affected by the openmp option and that creates resource underutilization. processors run idle when those steps are not being run. in my ad hoc analysis i have found i can process a single subject in about 5 hours using openmp 8, but that holds up 8 processors for that subject. the same subject can be processed in about 12 hours one 1 processor. say i have 16 processors, i can process 16 subjects in say 12 hours using 1 processor per recon. however, using 8 per recon would take about 40 hours, 2 subjects every 5 hours. so on our cluster, we tend to process with openmp 1 or 2 depending on the average load on the cluster. this is also dependent on your hardware, amount of memory, cluster scheduler, etc.,. if i really need speed on an individual case i go with -openmp 8. cheers, satra On Wed, Aug 20, 2014 at 11:04 AM, O'Shea,Andrew aos...@ufl.edu mailto:aos...@ufl.edu wrote: Hello all, Traditionally I have only processed FS data using a single core per person, but processing many people at once. Now we have caught up with the backlog of scans, we have a continuos trickle of scans coming in 1 by 1. I was wondering if anyone has tested how the speed-up of open-mp varies with number of cores used simultaneously. For example how much faster is using 100 cores versus 10? I am trying to find a sweet spot of resource usage and speed. Thanks! -Andrew ___ 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Fwd: Re: Open MP parallel processing scaling factor?
Opps... I forgot the attachment. Here it is. -Zeke Original Message Subject: Re: [Freesurfer] Open MP parallel processing scaling factor? Date: Wed, 20 Aug 2014 15:24:14 -0400 From: Z K zkauf...@nmr.mgh.harvard.edu To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu, Satrajit Ghosh sa...@mit.edu, aos...@ufl.edu Andrew, I basically agree with everything Satra is saying. Just as an added piece if info, Ive included a chart which did a systematic study of recon-all processing times with different number of cpus in parallel. These results are a bit old (and might be for low-res data) but the general idea is that there is a point of diminishing returns after using 4 processors in parallel. The gain from using more processors may be worth it for you. There are other tricks to getting faster recons (like processing left and right hemishperes in parallel) but that is a bit more tricky and requires a custom script. I can provide additional information if you think you would like to pursue that avenue -Zeke On 08/20/2014 11:21 AM, Satrajit Ghosh wrote: hi andrew, i haven't done many systematic comparisons but there are a few practical considerations to take into account. in recon-all, i believe a few steps are affected by the openmp option and that creates resource underutilization. processors run idle when those steps are not being run. in my ad hoc analysis i have found i can process a single subject in about 5 hours using openmp 8, but that holds up 8 processors for that subject. the same subject can be processed in about 12 hours one 1 processor. say i have 16 processors, i can process 16 subjects in say 12 hours using 1 processor per recon. however, using 8 per recon would take about 40 hours, 2 subjects every 5 hours. so on our cluster, we tend to process with openmp 1 or 2 depending on the average load on the cluster. this is also dependent on your hardware, amount of memory, cluster scheduler, etc.,. if i really need speed on an individual case i go with -openmp 8. cheers, satra On Wed, Aug 20, 2014 at 11:04 AM, O'Shea,Andrew aos...@ufl.edu mailto:aos...@ufl.edu wrote: Hello all, Traditionally I have only processed FS data using a single core per person, but processing many people at once. Now we have caught up with the backlog of scans, we have a continuos trickle of scans coming in 1 by 1. I was wondering if anyone has tested how the speed-up of open-mp varies with number of cores used simultaneously. For example how much faster is using 100 cores versus 10? I am trying to find a sweet spot of resource usage and speed. Thanks! -Andrew ___ 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 BrownCluster-4-1.pdf Description: Adobe PDF document ___ 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] bbregister for MRA
Hi Surfers I want to use bbregister to register my MRA scans to the structural scans. The first attempts by using these parameters came out OK but not perfect: bbregister --s Subject_ID --mov MRA.nii --init-fsl --reg register.dat --bold However, there are obvious problems around frontal areas. I have to admit that one of the reasons for this imperfect registration may be that MRA scans do not cover the whole brain. However, they still cover a large portion of it. I was wondering if there is any argument in bbregister command that may help me improve the quality. It is very fine if it increases the registration time. Regards P.S.: using --t2 in bbregister (instead of --bold) generated the same outcome but --t1 was completely off. -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School ___ 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] Extracting Group Means for Cortical Thickness
Dear Mailing List, I have just completed a QDEC (v5.1.0) analysis of the following design: Measure:thickness Smoothing (FWHM):10 Hemisphere:lh 2 Discrete (Fixed Factors):group (2 levels, AtRisk Control) and gene (2 levels, CC TTorTC) 1 Nuisance Factos:age On completion of the analysis, I have selected the following results in the display tab: Does the average thickness, acounting for group, differ between CC and TTorTC?. I have then completed an FDR correction by clicking the Set Using FDR (Rate 0.05) button. The following info is then printed to the terminal window: MRISfdr2vwth(): np = 163842, nv = 163842, fdr = 0.05, vwth=4.74798 Found 59 of 163842 vertices above FDR threshold (of 4.74798) I have then hit Find Clusters and Goto Max and found there to be a single cluster in the medialorbitofrontal, with a size of 26.09 mm2. I would now like to know what the mean thickness is for that cluster at each level of my gene variable. How can this information be obtained? -- Kind regards, Bronwyn Overs Research Assistant Neuroscience Research Australia Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia *M* 0411 308 769 *T* +61 2 9399 1883 *F* +61 2 9399 1265 neura.edu.au http://neura.edu.au Follow @neuraustralia on twitter https://twitter.com/neuraustraliaFollow NeuRA on facebook https://www.facebook.com/NeuroscienceResearchAustraliaSubscribe to the NeuRA Magazine http://www.neura.edu.au/help-research/subscribe ___ 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_tessellate: max vertices 1000000 exceeded
Thanks Zeke Bruce On Aug 20, 2014, at 1:55 PM, Z K zkauf...@nmr.mgh.harvard.edu wrote: Hello, The latest version of mri_tessellate can be downloaded using this the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_tessellate It would be wise to backup your existing version befor overwriting it with the version contained in the link above. -Zeke On 08/19/2014 05:52 PM, Michiel Kleinnijenhuis wrote: Hi, While doing a high resolution ex vivo recon job, I came across the error mri_tessellate: max vertices 100 exceeded As mentioned in the threads http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg35305.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35305.html http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31331.html there seems to be an easy fix. Does anyone have a compiled version of mri_tesselate with the vertex limit relaxed; for Mac (freesurfer-Darwin-lion-stable-pub-v5.3.0)? Thanks! Michiel Kleinnijenhuis == *Michiel Kleinnijenhuis* Postdoctoral researcher FMRIB Centre Nuffield Department of Clinical Neurosciences University of Oxford ___ 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 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] no improvement for recon-all result after edits
Hi I am reposting my message, hoping someone can give me some hint to get my problem solved. Thanks in advance!! On Mon, Aug 18, 2014 at 10:42 PM, Jidan Zhong jid...@gmail.com wrote: Hi Freesurfer experts, I was doing some manual editing on our subjects which are patients with lesions. I managed to correct most of them, however, 4 subjects have the same problem that I can't fix no matter what edits I tried. So, the 4 subjects, they all have the same problem, which is: frontal part of superior temporal gyrus region is not segmented as white matter, thus they are just missing from the final surfaces and final segmentations. But when just do eye check, there is nothing wrong with this part, even the intensity looks the same of other white matter parts.It's just suddenly cut. When I went back to those subjects, first I tried with control points. - It didnt help. I confirmed that white matter is present connected to the main brain white matter volume. -- I reran from recon-all autorecon2-wm, didnt help. Then I checked the aseg.mgz, that part is segmented as white matter correctly. I even modified the aseg.mgz (although not suggested), it still didn't work It is just weird that the surface was just cut from the middle of STG. So, is there any other way I can tell FreeSurfer that this is really STG and please keep it? Thanks!! -- Regards, Jidan -- 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.
