Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 discussions

How to get deformation maps in surface-based registrations
by Xiaojing Long 18 May '10

18 May '10

Hi, all, I have a question regarding how to get the deformation map in surface-based registration. I am wanting to use mris_register to align two surfaces. Can I get the deformation maps describing the vertex-to-vertex correspondence? How can I get it? Thanks a lot. Best, Xiaojing

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Re: [Freesurfer] Number of time pointsTuesday, May 18, 2010 12:17 PM
by Tadimeti, Usha 18 May '10

18 May '10

Hi Doug, Thank you very much for the reply. The question that I have now is, how do I distribute my time points between the events and also specify a fixed number of time points for the "NULL" cases? Thanks and Regards, Usha you should not interpret each line as a time point. Each line is a stimulus presentation. You have specified that the presentations are 1 sec long and can occur at an time divisible by 1 sec (--psdwin 0 12 1), so you could have as many as 600 lines. BTW, I would probably go longer than 12 sec for the window, more like 20 would be better. doug Tadimeti, Usha wrote: > Hi, > >> I was trying out a code to generate optimal sequences using optseq2. The code is as follows: >> >> >> optseq2 --ntp 300 --tr 2 \ >> --psdwin 0 12 1 \ >> --ev one 1 20 \ >> --ev two 1 15 \ >> --ev three 1 15 \ >> --ev four 1 50 \ >> --ev five 1 50 \ >> --ev six 1 50 \ >> --ev seven 1 50 \ >> --nkeep 2 \ >> --o ex \ >> --nsearch 10 >> >> The output file for the above code displays more than 300 lines,i.e., >300 time points. How can I modify the code so as to limit the output to 300 time points. Also, the output has all the required categories(events) till the end, Hence I could not just ignore the lines above 300. >> >> Thanks, >> Usha Tadimeti >> Biomedical Engineering Student >> Marquette University >> Milwaukee, Wisconsin >> usha.tadimeti(a)marquette.edu<http://us.mc344.mail.yahoo.com/mc/compose?to=usha.tadimeti@marquette.edu>

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Number of time points
by Tadimeti, Usha 18 May '10

18 May '10

Hi, > > I was trying out a code to generate optimal sequences using optseq2. The code is as follows: > > > optseq2 --ntp 300 --tr 2 \ > --psdwin 0 12 1 \ > --ev one 1 20 \ > --ev two 1 15 \ > --ev three 1 15 \ > --ev four 1 50 \ > --ev five 1 50 \ > --ev six 1 50 \ > --ev seven 1 50 \ > --nkeep 2 \ > --o ex \ > --nsearch 10 > > The output file for the above code displays more than 300 lines,i.e., >300 time points. How can I modify the code so as to limit the output to 300 time points. Also, the output has all the required categories(events) till the end, Hence I could not just ignore the lines above 300. > > Thanks, > Usha Tadimeti > Biomedical Engineering Student > Marquette University > Milwaukee, Wisconsin > usha.tadimeti(a)marquette.edu<http://us.mc344.mail.yahoo.com/mc/compose?to=usha.tadimeti@marquette.edu>

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mri_aparc2aseg on a custom annotation
by Martin Kavec 18 May '10

18 May '10

Hi, I have a problem using mri_aparc2aseg with a custom annotations containing labels created manually in tksurfer and exported. Basically, I would like to end up with a volume file similar as aparc+aseg.mgz but containing only a strip of a cortex corresponding to a label defined using tksurfer. The command I used is following: mri_aparc2aseg --s fsaverage --o labels.mgz --anot labels The command passes fine, but what I get is 2000 for all the cortical voxels, while I expected zeros for all the cortical voxels, except for those corresponding to the label. Any help on is greatly appreciated. Thanks, Martin

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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

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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

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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

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Freesurfer May 2010