Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30086 discussions

Freesurfer compatibility Fedora 12?
by Mohammed el Morabit 18 May '10

18 May '10

Hi FreeSurfer Experts, I am working on a cluster which ran until recently on the Linux OS Fedora 4. Since the upgrade to Fedora12 I can no longer launch tkmedit whereas it worked fine on the previous OS(fedora4). The following error appears: GLUT: Fatal Error in tkmedit.bin: visual with necessary capabilities not found. Any suggestions would be helpful Thanks in advance. Mohammed

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mergecontrasts-sess , does not work in my freesurfer
by caspari＠clipper.ens.fr 18 May '10

18 May '10

hello! I would like to mask different predefined contrasts in a way it is described by the mergecontrasts-sess command, and that best for my fixed effect group analysis! This command seemingly does not work, is there another possiblity/flag I could use? I use freesurfer version 4.5.0- I hope someone can help me with this. Nat

1 0

labels don't match with tkmedit and tksurfer
by Prapti Gautam 17 May '10

17 May '10

Dear FreeSurfers, I am having some problems creating a label in tksurfer and subsequently converting it into a volume file. I have created a custom label in a test subject using tksurfer which loads correctly onto the surface when viewed with tksurfer. However, when I load the label into tkmedit in the same subject - it seems to be labelling regions that are not on the surface of the brain, but lie somewhat haphazardly in the cortex near the surface. Do you know why this is happening? I further need to convert the label into a volume file and have used mri_label2vol to do this. Mri_label2vol -- label subject/label/pfc.label -temp subject/mri/brainmask.mgz --o subject/label/pfc.mgz However, perhaps since I can see that the label does not sit correctly on the surface in tkmedit, the volume file is also not on the cortical surface, but runs below it. Can anyone point me in the right direction as to where I might be going wrong? Thanks, Prapti

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areas to be excluded during manual corrections of pial and main surfaces
by Mehul Sampat 17 May '10

17 May '10

Hi Folks, On the FAQ, the response to one question says that the surfaces near the medial wall, hippocampus and amygdala are unreliable and should be excluded from a thickness analysis. The link for this is: http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Thesurface… My question is, as a rule of thumb, are there any other regions that should be excluded while doing manual corrections to pial and main surfaces ? For example, should we stop looking at the pial and main surfaces in the axial slices where the medulla is observed ? Basically, are there any other suggestions about which regions do not need corrections to the pial and main surfaces ? thanks Mehul

2 1

negative ICV volume
by Guang Zeng 17 May '10

17 May '10

Hi, there, Recently, I ran a subject through FreeSurfer 4.5.0. I load the segmentation results using tkmedit, it looks fine to me. But, from both aseg.stats and wmparc.stats, I read a negative ICV volume, # subjectname 01290403_20080924 # BrainMaskFile mri/brainmask.mgz # BrainMaskFileTimeStamp 2010/05/06 18:15:29 # Measure BrainMask, BrainMaskNVox, Number of Brain Mask Voxels, 1284740, unitless # Measure BrainMask, BrainMaskVol, Brain Mask Volume, 1284740.000000, mm^3 # Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles, 847219.000000, mm^3 # Measure BrainSeg, BrainSegNVox, Number of Brain Segmentation Voxels, 897849, unitless # Measure BrainSeg, BrainSegVol, Brain Segmentation Volume, 897849.000000, mm^3 # Measure IntraCranialVol, ICV, Intracranial Volume, -1057.998574, mm^3 Did anyone meet this kind of problem before? Thanks! Guang _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28…

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Freesurfer Linux Config Error
by Tina Jeon 17 May '10

17 May '10

Good afternoon, Hello Freesurfer gurus, I am running into an error when I use the visualization tools (i.e., tkmedit, tksurfer) in freesurfer and just wondering if you can shed some light on this. I am using Red Hat Linux Version 5.1 on the latest version of freesurfer. When I use the above commands I get the error: GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by display: :0.0 I am using the NVidia NV44 driver (Quadro NV5 285). Do I need to change the xorg.config file? And/or update the driver? Also when I use tkregister I get the error: Opening window subjid No glx extension! register: ### tkoInitWindow(name) failed The visualization tools previously ran flawlessly until I just revisited freesurfer after a 6 month hiatus. Let me know if you have any answers. Thank you in advance. Tina Jeon

1 0

Fsgd_DODS
by Kelly Silva 17 May '10

17 May '10

Hello, We are using the DODS model and we saw on the Freesurfer`s tutorial that we can create an fsgd with DODS contrast with 4 groups and 1 covariate. We have 3 groups and we want to use 1 or 2 covariates. Is it posible to run this analysis? If so, how can we do that? Thanks in advance and best regards, Kelly

2 1

Re: [Freesurfer] How to measure hippocampal volume
by Bruce Fischl 17 May '10

17 May '10

Hi Leonardo, the aseg.stats file will contain the relevant volumes. cheers Bruce On Mon, 17 May 2010, Leonardo Chesi wrote: > Hi, after your help, now I can segment my MRI images fine with the > nu_correct command. Now I'd like another little help from you. I study AD's > patients and I need to extract the hippocampal, the amygdala and another few > volumes from the segmented images. Can you help me? What kind of command I > can give to FreeSurfer to obtain this?, I have to use qdec? > > Thank a lot > > LEONARDO > >

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How to measure hippocampal volume
by Leonardo Chesi 17 May '10

17 May '10

Hi, after your help, now I can segment my MRI images fine with the nu_correct command. Now I'd like another little help from you. I study AD's patients and I need to extract the hippocampal, the amygdala and another few volumes from the segmented images. Can you help me? What kind of command I can give to FreeSurfer to obtain this?, I have to use qdec? Thank a lot LEONARDO

1 0

Hippocampus
by p.s.bjerkan＠studmed.uio.no 17 May '10

17 May '10

Hi, We have a paper under review where we have analyzed hippocampal volumes obtained by FreeSurfer version 3.0.2. One reviewer asks for the grey matter fraction of the hippocampus. The FreeSurfer aseg output provides only total volume for the various subcortical structures, so we asssume it's not possible to obtain grey or white matter fractions? Thank you! Petr S. Bjerkan

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