Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 discussions

fwhm vs. fwhm-surf in version 5.0
by Shahin 22 Aug '10

22 Aug '10

Hi, In version 5.0 it is mentioned that "- fwhm-surf" is obsolete (I know it is still available). I want to know what "- fwhm" option exactly do when I have already mentioned that I want a surface only processing (by using "-surface self lhrh"). Does it do smoothing on the basis of volume or surface and how significant the difference is? Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

How to add volume on pial surface in manual editting the trouble shootings
by 李瑾 22 Aug '10

22 Aug '10

Dear freesurferers I have faced a problem in editing pial surface in trouble shootings. Since the page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits has showed how to delete volume which is really useful, however, we faced another problem, that is how to add volume. I selected the edit voxels tool, tried to set Mode to "Clone" (Clone Source to "Aux Volume") and used the middle button on the mouse, but did not see any change on the main volume. The skull strip is fine, so I need not edit the skull strip, but some brain tissue was not included by the red line (represent the pial surface). Could anybody tell me how to add volume on pial surface in manual editting the trouble shootings? Thanks in advance! Jin

1 0

Binary masks from aparc+aseg.mgz
by Timothy Vickery 21 Aug '10

21 Aug '10

Hi all, I'm creating binary mask volumes in a subject's native functional space from the segmented brain in aparc+aseg.mgz (FS v 4.5). I have found that doing this two different ways produces different results, and I'm wondering if anyone can illuminate why this might occur and which method is more appropriate (or what other method you would suggest)... Method 1: Resample aparc+aseg.mgz into native functional space using mri_label2vol --seg aparc_aseg.mgz --fillthresh 0.5 [...plus the rest of the appropriate inputs such as subject's bold/register.dat] Then I just parse the resulting image (using matlab or python code) into separate binary masks for each unique identifier that I'm using...E.g., for right IPL I load this image and create a new volume [newVol = (oldVol==2008)] and save that out. Method 2: Create a label file from aparc+aseg.mgz for each unique identifier that I'm using, and then use mri_label2vol to produce a binary mask in native functional space: mri_cor2label --i aparc+aseg.mgz --id 2008 --l rIPL.label mri_label2vol --label rIPL.label --fillthresh 0.5 [... plus the rest of the required inputs, same as those used in Method 1] Even though these seem like they should be equivalent to me, and although the masks produced agree for the most part, I generally get several more voxels per ROI using Method 2 than I do using Method 1 (and not complete overlap otherwise). For instance, for one subject, Method 1 yields 308 voxels in rIPL, but Method 2 yields 316 voxels; disagreement between the two occurs in a total of 26 of those voxels, so it isn't just a matter of Method 2 being more generous. The discrepancy seems to be proportional to the size of the ROI, so I get just a handful of disagreements for smaller ROIs (but it seems to happen almost all the time). Thanks for any advice on which method is better, or a suggestion of a better method. Best, Tim

2 4

ICV volume and 1.5T x 3.0T
by Tadeu Kubo 20 Aug '10

20 Aug '10

Hi FS, I have two important doubts... Is it the CSF volume included in the ICV volume (aseg.stats)? Is it possible include in the same group patient acquired from 1.5T and 3.0T? Do you have an article about this topic? TK

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Volume to surface dimension mismatch
by Lena Palaniyappan 20 Aug '10

20 Aug '10

I have a mask file which I need to overlay on the individual images of a group of subjects to extract thickness values within ht mask. But the mask is of dimension 2X2X2, will this be an issue? Thanks Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

2 3

FreeSurferAlpha Label Volumes
by Mona 20 Aug '10

20 Aug '10

Hello, I'd like to extract hippocampal and PHC volumes from files reconstructed with FreeSurferAlpha. Is there a command for this or would you recommend re-reconstructing to obtain label volumes? Thank you, Mona

3 2

Automatic Plotting of Hemodynamic Response???
by Adam Nitenson 20 Aug '10

20 Aug '10

Hello Freesurfers, I am currently running ROI analyses (dACC) and want to plot the timecourse of hemodynamic responses to a cognitive task (2 conditions) in a group of subjects. I have been using func2roi commands such as func2roi-sess -roidef lh_dACC -analysis RM_correct_error -anatlabel lh.dACC -maskcontrast error_vs_correct -maskthresh 0.000000001 -masktail pos -maskframe 5 -maskmap sig -sf /autofs/space/ventzl_036/users/RespMon12C/subject_lists/caitlin_SZerrorcorrect.txt -d /autofs/space/ventzl_036/users/RespMon12C/subjects and then roisummary to generate charts from which I create a hemodynamic curve through data manipulation. I was recently informed that there should be a way through which I could automatically plot such a hemodynamic curve, and that this method might not require a designated threshold as func2roi does (as we want any activation in the ROI to be considered). Is there any way to create a more automatic, streamlined hemodynamic response curve, or are func2roi and roisummary the standard means of doing this? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

2 1

mirror hemispheres
by johanna feiler 20 Aug '10

20 Aug '10

Hello FreeSurfers, I wonder if it is possible to mirror my complete data, so that the right hemisphere will be the left one and the other way round. I was thinking about using this command: fslswapdim <input> z -x -y <output and start with all the preprocessing steps afterwards. I want to use it for anatomical data only, so the question is if it will work with Freesurfer (not FSL) as well? Do you think it would work this way anyway? Or has anybody any other experiences with mirroring data? Any help will be appreciated! Best regards, Johanna Feiler ___________________________________________________________ Neu: WEB.DE De-Mail - Einfach wie E-Mail, sicher wie ein Brief! Jetzt De-Mail-Adresse reservieren: https://produkte.web.de/go/demail02

2 1

whoops
by Adam Nitenson 19 Aug '10

19 Aug '10

Sorry for the double post (and, I suppose, the triple post as well) Only consider the more recent email, and it's just a completed version of my first one. Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

1 0

Automatic Plotting of Hemodynamic Response???
by Adam Nitenson 19 Aug '10

19 Aug '10

Hello Freesurfers, I am currently using func2roi to analyze the hemodynamic response to a cognitive task within the dACC in a group of subjects. I have been constraining my analyses to 6 seconds post stimulus onset, a specific contrast (error_vs_correct), and with a very low threshold so that any activation in the area will be considered. Here is an example of a command that I have been using. func2roi-sess -roidef lh_dACC -analysis RM_correct_error -anatlabel lh.dACC -maskcontrast error_vs_correct -maskthresh 0.000000001 -masktail pos -maskframe 5 -maskmap sig -sf /autofs/space/ventzl_036/users/RespMon12C/subject_lists/caitlin_SZerrorcorrect.txt -d /autofs/space/ventzl_036/users/RespMon12C/subjects I then use roisummary-sess to generate charts of the results, and futher data organization allows me to plot the hemodynamic response curve. However, I was recently told that there should be a way to automatically generate such curves; a method that also does not require a maskthresh as func2roi does (as we essentially do not want any threshold). Are there any techniques, Freesurfer or otherwise, that might allow me to conduct such analyses in a more streamlined fashion, or is func2roi the standby command for such tasks? Thanks! Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital

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Freesurfer August 2010