Freesurfer September 2014

freesurfer@nmr.mgh.harvard.edu

120 participants
164 discussions

Boston FreeSurfer Course
by Allison Stevens 01 Oct '14

01 Oct '14

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

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Two questions: 1. Regarding ASEG and reduced FOV; 2. Regarding ventral diencephalon contents
by Matthew Sacchet 01 Oct '14

01 Oct '14

Hi all, I was hoping to gain insight regarding two questions associated with the use of FreeSurfer's aseg (Fischl, Neuron 2002): 1. I have been using aseg to assess volumetric differences across populations. For one of our individuals a portion of the right hemisphere was not fully collected. The entirety of the subcortical structures we are interested in were collected (I've attached an image to this message, not sure if images propagate to the list...). Will the lack of whole-brain coverage bias the segmentation for the hemisphere that was not fully collected? I'm assuming that the fully covered hemisphere's data will be ok. 2. Regarding the "ventral diencephalon" region that is segmented using aseg, is there a 'gold standard' citation that describes what anatomical structures are included in this region? Previously on the FreeSurfer list serve there was mention from Anderson Winkler that the VD includes "The region defined as ventral diencephalon is very heterogeneous and I would not classify it either as GM or WM, as it includes mamillary bodies, tuber cinereum/infundibulum (but not hypophysis), some hypothalamic nuclei near the lateral and inferior walls of the 3rd ventricle and sometimes fragments of the optic tracts (but not chiasm, which has its own label). It also includes parts of the mesencephalon (e.g. part of the cerebral crux, part of the substantia nigra and rubra)", but no citation was given. In Glahn et al. (Biological Psychiatry 2012 71, 6-14) it is stated that the VD mostly includes the hypothalamus, but again, as far as I can tell, a citation is not offered. Any help would be appreciated, thank you, Matthew

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Problems with manual grey matter editing
by Zamroziewicz, Marta Karolina 01 Oct '14

01 Oct '14

Hello, We have some reconstructions with a significant amount of grey matter excluded in the temporal cortex and are having problems using manual voxel editing to fix this. Our correction process for brain tissue that wasn’t included in the pial/white matter outlines has been as follows: 1. When white matter is excluded from the white matter outline, we’ve used control points to identify missed white matter. We then re-run using the following command: recon-all -autorecon2-cp -autorecon3 -subjid <SUB_ID>. 2. When grey matter is excluded from the pial outline, we first make sure that white matter is outlined appropriately. If adding control points doesn’t fix the grey matter problem, we manually add grey matter voxels to the brainmask volume using the voxel edit tool. We then re-run using the following command: recon-all -autorecon-pial -subjid <SUB_ID>. In some cases (especially in the temporal cortex), the new reconstructions don’t incorporate the manually added grey matter voxels into the pial outline. I’ve attached an image of a subject who didn’t have white matter problems but did have excluded grey matter in the temporal cortex. We reran this subject using the recon-all -autorecon-pial -subjid <SUB_ID> command and the newly added grey matter voxels weren’t included in the new pial outline. Is there a way to address this problem? Thank you very much for your time! Marta _________________________________ Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzamro2(a)illinois.edu<mailto:mzamro2@illinois.edu> 815-980-3882 _________________________________ [cid:5F7AEAD8-4EA8-49CB-A4C2-7502236F5F01@beckman.uiuc.edu]

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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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Freesurfer September 2014