Freesurfer

freesurfer@nmr.mgh.harvard.edu

3 participants
30135 discussions

display thickness map in freeview
by Harms, Michael 01 Oct '14

01 Oct '14

2 1

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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create a label file in tkmedit
by Adam, Ruth 01 Oct '14

01 Oct '14

Hi all, I am creating a label file using the select voxels tool in TkMedit. However this doesn't work properly with e.g. all saved vertex IDs are set to -1. Example file: #!ascii label ….. , from subject ….. vox2ras=TkReg 19 -1 -40.000 52.000 21.000 110.0000000000 -1 -39.000 52.000 21.000 110.0000000000 -1 -38.000 52.000 21.000 110.0000000000 -1 -37.000 52.000 21.000 110.0000000000 -1 -37.000 52.000 19.000 110.0000000000 -1 -37.000 52.000 17.000 102.0000000000 -1 -38.000 52.000 17.000 108.0000000000 -1 -39.000 52.000 18.000 110.0000000000 -1 -39.000 52.000 19.000 110.0000000000 -1 -39.000 52.000 20.000 110.0000000000 -1 -38.000 52.000 20.000 110.0000000000 -1 -38.000 52.000 19.000 110.0000000000 -1 -38.000 52.000 23.000 110.0000000000 -1 -38.000 52.000 22.000 110.0000000000 -1 -37.000 52.000 22.000 109.0000000000 -1 -37.000 52.000 20.000 110.0000000000 -1 -39.000 52.000 22.000 110.0000000000 -1 -39.000 52.000 24.000 108.0000000000 -1 -39.000 52.000 23.000 110.0000000000 Any ideas how this can be solved? Many thanks in advance! Best, ruthi

2 1

make movies of non eeg/meg temporal data ?
by Gregory Kirk 01 Oct '14

01 Oct '14

I would like to make a movie of the temporal evolution of data on the cortical surface from something im doing. similar to what mne_make_movie does, but it's not eeg/meg data. is there a way to make and display movies of data in tksurfer or freeview ? or i guess i could `trick` mne and display my data in the mne package viewer ? any ideas on what is the easiest/best way to skin this cat ? thanks Greg

3 2

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]

2 1

Can't set values in tksurfer "Phase encoded data display" window
by Andre Salles Cunha Peres 30 Sep '14

30 Sep '14

Hello, I'm working with retinotopic maps, and how my experiments was with polar stimulus I want to change the angle cycles to 2 in tksurfer, however it is impossible to change the values in the "Phase encoded data display" window (View>Configure>Phase encoded data display). I can select the text in the edit text, however when I type the new value, nothing happens. Could someone help me? Thanks, Andre Salles Cunha Peres Federal University of Rio Grande do Norte Brain Institute http://www.neuro.ufrn.br/?lang=en Av. Nascimento de Castro, 2155 59056-450 - Natal / RN

1 0

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

2 5

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

30 Sep '14

2 2

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

2 1

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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