Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

bbregister for MRA
by SHAHIN NASR 30 Sep '14

30 Sep '14

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

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pial surface crossing white
by Harms, Michael 30 Sep '14

30 Sep '14

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Righty and left hemispheric white matter volume
by Alshikho, Mohamad J. 30 Sep '14

30 Sep '14

Dear FS Experts, I am beginner in FS and I need you precious advice... In order to compare the volume of the right and left hemispheric white matter in my dataset (29 controls 23 patients). I did recon_all for my T1 data then I used the volume of the Left and right cerebral white matter which are included in "aseg.stats" to run my statistical analysis. Kindly, is this procedure correct? Thanks in advance, Mohamad

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Re: [Freesurfer] Out of memory error on mri_cvs_register
by Lilla Zollei 30 Sep '14

30 Sep '14

Hi Mohammadi-Nejad, The creation of the non-linear deformation field will require more memory than what you currently have and that is causing the problem. Is there any way you can assign twice (or at least 1.5x) as much memory to this process as you are currently using? Lilla On Mon, 29 Sep 2014, Ali-Reza Mohammadi-Nejad wrote: > Thank you! > The command is : "mri_cvs_register --mov 001 --template 000". > The error is: > [0]PETSC ERROR: --------------------- Error Message ------------------------------------ > [0]PETSC ERROR: Out of memory. This could be due to allocating > [0]PETSC ERROR: too large an object or bleeding by not properly > [0]PETSC ERROR: destroying unneeded objects. > [0]PETSC ERROR: Memory allocated 0 Memory used by process -2147483648 > [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. > [0]PETSC ERROR: Memory requested 2391628012! > > Also in the attached file you can find the log of this command. > > Best regards, > Mohammadi-Nejad > > > > On Monday, September 29, 2014 2:12 PM, Lilla Zollei <lzollei(a)nmr.mgh.harvard.edu> wrote: > > > > 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 > > > > > > > > > > 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. > > >

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Re: [Freesurfer] Overclocking CPU for Freesurfer
by Jonca, Jacek 30 Sep '14

30 Sep '14

As Matt pointed out for as long as you achieve a stable overclock and have ample cooling for the CPU and memory freesurfer (and any other programs) will run just fine. I used to run subjects on Intel Q6600 overclocked from 2.8ghz to 3.4ghz with a push-pull cooling solution and had no problems. Greetings, Jacek Jońca-Jasiński [TTU_DblT_fl4C] Jacek Jońca-Jasiński, Ph.D. Director The Graduate School Administration Bldg 328 / 40D | 2625 Memorial Circle Box 41030 | Lubbock, TX 79409-1030 T 806.834.3348 | F 806.742.4038 ---------- Forwarded message ---------- From: Chiu, Bryan (PHTH) <bryan.chiu(a)ubc.ca<mailto:bryan.chiu@ubc.ca>> Date: Mon, Sep 29, 2014 at 4:26 PM Subject: [Freesurfer] Overclocking CPU for Freesurfer To: "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> 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(a)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.

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LME Models
by Karishma Smart 30 Sep '14

30 Sep '14

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

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Re: [Freesurfer] Overclocking CPU for Freesurfer
by Matt Glasser 29 Sep '14

29 Sep '14

It will just run faster so long as things like memtest86 and prime95 don¹t have errors. Peace, Matt. From: "Chiu, Bryan (PHTH)" <bryan.chiu(a)ubc.ca> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, September 29, 2014 at 4:26 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)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(a)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.

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Overclocking CPU for Freesurfer
by Chiu, Bryan (PHTH) 29 Sep '14

29 Sep '14

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

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Pial Surface Incorrect For Native T1
by Zachary Greenberg 29 Sep '14

29 Sep '14

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

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mri_watershed problems
by Sam Zorowitz 29 Sep '14

29 Sep '14

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

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