[Freesurfer] Transform MNI-space segmentation into Subject-space
Hello I have a segmentation which made on MNI space, is it possible to do the inverse transform to the segmentation from MNI space to each subject space? does the size of the MNI segmentation (218*182*182) should be a problam? I was traing : mri_vol2surf MNI_Segmentation.nii --hemi lh --regheader bert --o /home/cnilab/ProgramFiles/freesurfer/NewFileName.mgz but i get a empty file. is there a diffrante way to do this? thanks. roy ___ 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] Out of memory error on mri_cvs_register
Hi I am trying to do an mri_cvs_register for two subjects analyzed with FS-5.1.0 on a 64-bit CentOS linux vmware on a 64 bit windows 7 with 16GB memory. I am running a signle mri_cvs_register and after certain time the process terminates with out of memory error. I have done this work a lot of times with different preprocessed subjects. Could you please let me to know that, How can I solve this problem? Best regards, Mohammadi-Nejad ___ 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] Out of memory error on mri_cvs_register
Hi Mohammadi-Nejad, Could you include the command that you submitted and the error message and log file from when the process terminated? Lilla On Mon, 29 Sep 2014, Ali-Reza Mohammadi-Nejad wrote: Hi I am trying to do an mri_cvs_register for two subjects analyzed with FS-5.1.0 on a 64-bit CentOS linux vmware on a 64 bit windows 7 with 16GB memory. I am running a signle mri_cvs_register and after certain time the process terminates with out of memory error. I have done this work a lot of times with different preprocessed subjects. Could you please let me to know that, How can I solve this problem? Best regards, Mohammadi-Nejad ___ 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] Boston FreeSurfer Course
Hello everyone, The next FreeSurfer Course will be held October 27th-29th at the Martinos Center in Charlestown, Massachusetts. Registration for the course is now open: https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription **Important: If we do not get at least 40 registrants for this course, we will have to cancel it. Details about the content of the course, the location, registration fees, accepted payment types, and nearby hotels is currently on the website above. Please read the above page in its entirety before registering and before sending questions. This course will contain a Diffusion analysis component. fMRI analysis will *not* be taught. Registration is first-come, first-serve. If you are not one of the first 50 to register, you will be put on a waiting list and will be notified if a spot becomes available. *Do not submit a payment or make travel arrangements until you have received an *email confirmation* that you successfully registered for the course. Allison Stevens Lab Manager FreeSurfer Development Team Laboratory for Computational Neuroimaging Massachusetts General Hospital Athinoula A. Martinos Center for Biomedical Imaging Bldg. 149, 13th Street, CNY 2301 Charlestown, MA 02129 ___ 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] pial surface crossing white
Hi Mike that's really strange. Are you sure you recreated the pial??? Can you double check time-stamps and such? And Euler number to make sure that it is the same for white and pial? If that all looks right, upload the subject and send me the command line you used for the rerunning and I'll investigate. cheers Bruce On Wed, 24 Sep 2014, Harms, Michael wrote: Hi, We are seeing some instances where the pial surface is crossing over the white surface in the vicinity of the precuneus and lingual cortex, where there is only a thin strand of WM separating the GM from the lateral ventricle. In these cases, it appears that GM is getting labeled as WM-hypointensities in the aseg, and then assigned a value of 250 in the wm.mgz. So, we deleted those erroneous values in the wm.mgz (changing them from 250 to 1). The resulting white surfaces following these edits are a much better reflection of where the white surface should be, but the pial surface still crosses over into the WM. See attached png's for examples in two subject, where there are both PreWMedit and PostWMedit snapshots for each of the two subjects. (In each of the attached examples, the issue is on the left hemi -- i.e,. right side of the snapshot). My question is: Is there some other way that we are supposed to edit this? Or, having fixed the gross errors in the white surface, do we just have to accept the remaining inaccuracy in the pial surface. It's a fairly localized remaining error in the pial surface, but I'm puzzled how it ends up on the wrong side of the white surface to begin with. thanks, -MH -- Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave. Tel: 314-747-6173 St. Louis, MO 63110 Email: mha...@wustl.edu The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] LME Models
Dear Freesurfers, This is a repeat question as either I did not see the response to the intial query (I apologise in that case!) or it was never answered. I am planning to do a longitudinal analysis. After I have processed the data through a longitudinal stream, should I use the LME model? I understand it is the most highly recommended for a comprehensive analysis; however the Freesurfer webpage says it is for univariate and mass-univariate analyses only. I would like to do a multivariate analysis. Can I still use the Matlab LME model? If not, is there an alternative way to do this? Any help would be appreciated! Thanks! Karishma -- Karishma Smart B.A. Biological Sciences Cornell University Class of 2013 Boston University School of Graduate Medical Sciences Class of 2015 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] how to deal with a big brain lesion?
Hi FreeSurfer experts, I happen to have a participant whose brain lesion from stroke (hemorrhage) distributed over a wide area. Therefore, the recon-all result is showing a big whole, about half a size of the cortex, on the anterior part of the left hemisphere corresponding to the lesion site. When I checked the previous mails, it is recommended to edit the WM volume for the whole caused by lesions: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/WhiteMatterEdits_freeview But because the size of the lesion is so big, involving more than 100 slides coronally, the process to fill the lesion area by Voxel Edit will be as long as tracing the lesion manually slide by slide. I wonder if you would have other suggestions to correct such a big geometric accuracy. Please let me know if you need other info. Thank you so much for your help! -Abel ___ 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 problems
Dear Freesurfer community, I am running into issues with mri_watershed, which I am using the create the BEM surfaces. In testing different preflooding height threshold (recommended for accurate skull-stripping), I am running into the issues that an -h 56 produces results where the cerebellum is stripped away, but -h 57 leaves far too much non-brain material in the image. As a result, my BEM surfaces are unrepresentative of the brain (either shrunken in or enlarged). I do, however, already have a satisfying brain-mask. Is there a way to pass the brain mask to mri_watershed to create new BEM surfaces without it creating a new brain mask? Sam Zorowitz Clinical Research Coordinator Division of Neurotherapeutics Department of Psychiatry: Neurosciences Massachusetts General Hospital 149 13th Street, Rm 2620e Charlestown, MA 02129 ___ 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] Transform MNI-space segmentation into Subject-space
You need to create a registration between your subject and your MNI space. Try using spmregister or fslregister (but not bbregister). But there is a bigger problem in that surface-sampling of ROIs in MNI space tends not to do very well, but I'll leave that up to you to evaluate On 09/29/2014 04:03 AM, Roy Talman wrote: Hello I have a segmentation which made on MNI space, is it possible to do the inverse transform to the segmentation from MNI space to each subject space? does the size of the MNI segmentation (218*182*182) should be a problam? I was traing : mri_vol2surf MNI_Segmentation.nii --hemi lh --regheader bert --o /home/cnilab/ProgramFiles/freesurfer/NewFileName.mgz but i get a empty file. is there a diffrante way to do this? thanks. roy ___ 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] Pial Surface Incorrect For Native T1
Hi Doug, Thanks for your continued help with this. I use freeview -v rawavg.mgz -f lh.pial.native The problem I was mentioning in my first message though, is that the native pial surface mesh output from mri_surf2surf is only oriented correctly in freeview, but not in any other mesh viewer (such as Matlab, Blender, Unity, Pyqt, etc...). For example, if I convert the lh.pial.native mesh to ascii with mris_convert lh.pial.native lh.pial.native.asc, I can then use all the tri and vert coordinates from that ascii file to plot the mesh in matlab (or some other viewer by converting the .asc to .obj). Viewing the Mesh in any of those third party methods will reveal that the mesh is flipped (left is right, so loading the left hem coords reveals the right hem) and oriented such that the respective poles of the brain (frontal and occipital) are pointing superior and inferior as apposed to a-p. This is where I'm stumped. Does freeview do something to remap the left-right flip and orient the mesh correctly? Thanks again. -zack On Wed, Sep 24, 2014 at 8:48 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: When I run your commands, the pial is correctly oriented and placed. What is your freeview command? This is what I use freeview -v rawavg.mgz --surface ../surf/lh.pial.native:edgecolor=yellow On 09/23/2014 06:11 PM, Zachary Greenberg wrote: Hi Doug, Thanks for getting back to me and sorry for the delay. Yes I can actually. If I corregister the CT to orig.nii and then pick out the points in freeview they look pretty good. This is a pretty painful process though. Is there an easy way to save a set of points in a text file from freeview? Ideally, I would like to be able to do this with the native pial surface as well, but I still have the problem of it appearing rotated and flipped in freeview. Is there a way to fix this? Thanks again for your help, Best, -Zack On Thu, Sep 18, 2014 at 12:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you get it to display correctly on the pial surface in conformed space? On 09/17/2014 08:04 PM, Zachary Greenberg wrote: Hello Freesurfer experts, I am having a tough time getting my pial surfaces into the correct anatomical space. I work with ECoG Patients, so we have pre-implant high resolution T1s (GE SPGR), and post-implant high resolution CTs that show the location of ECoG electrodes within the patient's skull. Our goal: display ECoG electrodes in their correct positions on the patient's native pial surface. Right now, my pipeline works like this: -ACPC align the T1, leave it in LAS orientation. -recon-all the acpc T1, using -3T -all -openmp 8 -use-gpu -corregister the CT to the acpc T1 (SPM), get electrode coords in T1 space -plot the electrodes on the resultant .pial surface from freesurfer The problem is, I can definitely tell that the position of the pial mesh is off (probably by 10 millimeters or so), as the electrodes (which have the correct coordinates from the T1 correg, confirmed visually by overlaying the CT on T1) are not in their correct positions on the mesh. Likewise, DTI fibers reconstructed from EPIs correctly corregistered to the T1 also appear off position within the .pial mesh. Here is what I have tried: compute the transform from .pial to .pial.native as suggested on https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat --noedit --regheader mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname This results in a mesh that is flipped (left is right) and rotated such that anterior is inferior (frontal cortex is pointing downward). The mesh appears this way when plotted in any viewer besides freesurfer (MATLAB mesh, Pyqt) but appears in the correct orientation in freeview. Replacing orig.mgz with the original T1.nii in the command above produces the opposite effect, freeview plots the orientation wrong, and any other viewer plots the Mesh oriented correctly, and the mesh appears to be identical to the originally output .pial mesh (electrodes are still wrong). Any help in pin pointing what is going wrong here would be greatly appreciated. I have a feeling it has something to do with the mesh being in surface RAS and the original T1 being in LAS. Thanks a bunch, -Zack ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] Pial Surface Incorrect For Native T1
Another note, I just did a little experimenting, and it appears that using a RAS oriented image for the initial recon-all run (I've been using all LAS images) will fix the left-right flipping that occurs with mri_surf2surf. However the mesh is still oriented incorrectly, such that a-p is facing superior-inferiror. -zack On Mon, Sep 29, 2014 at 1:07 PM, Zachary Greenberg zacharyigreenb...@gmail.com wrote: Hi Doug, Thanks for your continued help with this. I use freeview -v rawavg.mgz -f lh.pial.native The problem I was mentioning in my first message though, is that the native pial surface mesh output from mri_surf2surf is only oriented correctly in freeview, but not in any other mesh viewer (such as Matlab, Blender, Unity, Pyqt, etc...). For example, if I convert the lh.pial.native mesh to ascii with mris_convert lh.pial.native lh.pial.native.asc, I can then use all the tri and vert coordinates from that ascii file to plot the mesh in matlab (or some other viewer by converting the .asc to .obj). Viewing the Mesh in any of those third party methods will reveal that the mesh is flipped (left is right, so loading the left hem coords reveals the right hem) and oriented such that the respective poles of the brain (frontal and occipital) are pointing superior and inferior as apposed to a-p. This is where I'm stumped. Does freeview do something to remap the left-right flip and orient the mesh correctly? Thanks again. -zack On Wed, Sep 24, 2014 at 8:48 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: When I run your commands, the pial is correctly oriented and placed. What is your freeview command? This is what I use freeview -v rawavg.mgz --surface ../surf/lh.pial.native:edgecolor=yellow On 09/23/2014 06:11 PM, Zachary Greenberg wrote: Hi Doug, Thanks for getting back to me and sorry for the delay. Yes I can actually. If I corregister the CT to orig.nii and then pick out the points in freeview they look pretty good. This is a pretty painful process though. Is there an easy way to save a set of points in a text file from freeview? Ideally, I would like to be able to do this with the native pial surface as well, but I still have the problem of it appearing rotated and flipped in freeview. Is there a way to fix this? Thanks again for your help, Best, -Zack On Thu, Sep 18, 2014 at 12:50 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Can you get it to display correctly on the pial surface in conformed space? On 09/17/2014 08:04 PM, Zachary Greenberg wrote: Hello Freesurfer experts, I am having a tough time getting my pial surfaces into the correct anatomical space. I work with ECoG Patients, so we have pre-implant high resolution T1s (GE SPGR), and post-implant high resolution CTs that show the location of ECoG electrodes within the patient's skull. Our goal: display ECoG electrodes in their correct positions on the patient's native pial surface. Right now, my pipeline works like this: -ACPC align the T1, leave it in LAS orientation. -recon-all the acpc T1, using -3T -all -openmp 8 -use-gpu -corregister the CT to the acpc T1 (SPM), get electrode coords in T1 space -plot the electrodes on the resultant .pial surface from freesurfer The problem is, I can definitely tell that the position of the pial mesh is off (probably by 10 millimeters or so), as the electrodes (which have the correct coordinates from the T1 correg, confirmed visually by overlaying the CT on T1) are not in their correct positions on the mesh. Likewise, DTI fibers reconstructed from EPIs correctly corregistered to the T1 also appear off position within the .pial mesh. Here is what I have tried: compute the transform from .pial to .pial.native as suggested on https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat tkregister2 --mov rawavg.mgz --targ orig.mgz --reg register.native.dat --noedit --regheader mri_surf2surf --sval-xyz pial --reg register.native.dat rawavg.mgz --tval lh.pial.native --tval-xyz --hemi lh --s subjectname This results in a mesh that is flipped (left is right) and rotated such that anterior is inferior (frontal cortex is pointing downward). The mesh appears this way when plotted in any viewer besides freesurfer (MATLAB mesh, Pyqt) but appears in the correct orientation in freeview. Replacing orig.mgz with the original T1.nii in the command above produces the opposite effect, freeview plots the orientation wrong, and any other viewer plots the Mesh oriented correctly, and the mesh appears to be identical to the originally output .pial mesh (electrodes are still
[Freesurfer] Overclocking CPU for Freesurfer
Hi, Is anyone aware of any issues that arise from overclocking and using Freesurfer? I was looking to see how much it would speed up recon-all with OpenMP using a stable overclock. ___ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia ___ 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] Overclocking CPU for Freesurfer
It will just run faster so long as things like memtest86 and prime95 don¹t have errors. Peace, Matt. From: Chiu, Bryan (PHTH) bryan.c...@ubc.ca Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Monday, September 29, 2014 at 4:26 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Overclocking CPU for Freesurfer Hi, Is anyone aware of any issues that arise from overclocking and using Freesurfer? I was looking to see how much it would speed up recon-all with OpenMP using a stable overclock. ___ Bryan Chiu Undergraduate Research Assistant Aging, Mobility, and Cognitive Neuroscience Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy Faculty of Medicine University of British Columbia ___ 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.
