Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

AC/PC positions and other questions
by François Tadel 12 Jul '13

12 Jul '13

Dear freesurfers, I'm working on a function to import automatically the segmentation folder into a Brainstorm database. I have a few questions: - Is there a way to read/get the position of the anterior and posterior commissures (AC/PC)? - What file should I read to get the labels corresponding to the aseg.mgz file? - Is there an easy way to generate surfaces for all the regions defined in aseg.mgz? - How do you create a mesh from a volume mask? Thanks, Francois

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Xhemi results
by amirhossein manzouri 12 Jul '13

12 Jul '13

Dear Doug and FS experts, I am trying to use Xhemi tool to study asymmetry in the brain. I have done the exact procedure you mentioned in WiKi for a group of 40 controls. 1) Is lh.lh-rh.thickness.sm00.mgh the stack of voxel-wise cortical thickness difference between left and right hemisphere of each subject? 2) If yes, shouldn't I see the similar mapping by overlaying this to lh and rh? (tksurfer fsaverage_sym rh inflated -aparc -overlay lh.lh-rh.thickness.sm00.mgh) 3) How do you interpret the result after analyzing within one group? ( tksurfer fsaverage_sym lh inflated -aparc -overlay glm.lh.lh-rh.thickness.sm05/osgm/sig.mgh) 4) Is there any way to look at the results through the brain per slice and also the whole brain? -- Best regards, Amirhossein Manzouri

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large SD of aparc in one group
by L. Koenders 12 Jul '13

12 Jul '13

Dear FreeSurfer experts, We have a question regarding the aparc output from the stats files, and hopefulle you can help us. We have 4 independent groups, of about 30 subjects per group, all scanned using the same protocal on the same MRI scanner. We ran the cross sectional FreeSurfer (5.2.0, Linux centos4_x86_64) pipeline, and extracted the volume information per person from the .stat files using Matlab. We transfered the volume information into SPSS, to calculate the Means and Standard Deviations per group. We are interested in a couple of regions of interest (anterior + posterior cingulate, OFC, parahippocamus and insula). What strange is though, it that the means and standard deviations of 3 groups are comparable across all regions, but the SDs of 1 group are very (very!) large. This is not a group in which we expect brain atrophy or anything like that. Below you see the SD values of all groups, with SD values up to four times bigger in group 1! 1 2 3 4 caudal ACC 618 516 643 589 rostral ACC 1583 578 692 623 PCC 1942 721 616 749 OFC 2632 1345 1844 1652 parahip 1198 346 271 394 insula 1410 1033 1096 1017 The outliers are different subject in every region, and I checked the parcellation output of them, that looks fine. We are wondering what could be the cause of this, do you have any ideas? Thank you in advance, Kind regards, Laura ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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Adjust lighting in Freeview
by Martijn Steenwijk 12 Jul '13

12 Jul '13

Hi all, Is there a way to ajust the camera lighting / add lights in Freeview? Currently the lighthing is such that the surface with normal pointing upwards are illuminated well, but the surface with normal pointing downwards not that good. Thanks for replies in advance, Martijn

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Pearsons r / adj. r squared
by Martijn Steenwijk 12 Jul '13

12 Jul '13

Dear all, Is there a way in freesurfer to compute surface wise pearsons r (for simple correlations) or adjusted r square / the vertex-wise explained variance for a GLM? Best, Martijn

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Multi Modality Data Orientation
by Barron, Daniel S 11 Jul '13

11 Jul '13

Dear Freesurfers, I am trying to perform probabilistic tractography (FSL Probtrackx) between seed and target VOIs made with Freesurfer's recon-all (T1) and dt_recon (DW) pipelines. I have the original T1 DICOMs, however, I only have the DW NIFTI image volumes. I do not know how the DW DICOMS were converted to NIFTI and am worried about L-R flipping. Within Mango, I have found the T1 images converted with mri_convert are (X+,Y-,Z+). The DW NIFTI is (Y-,Z-,X-). mri_info gives me a lot of information that, unfortunately, I do not entirely understand. Can you recommend a way for me to verify consistent orientation in both my T1 and DW images? Thank you! Cheers, Daniel

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How to fix grey matter boundary
by Giusy Chinnici 11 Jul '13

11 Jul '13

Dear developers, I'm working with patients affected by cortical focal dysplasia; images of these patients often show thickening in some areas of the cortex. In many cases the reconstruction of the pial boundary is not accurate. I have been trying to correct this boundary but I couldn't understand the procedure. I have already checked accuracy and intensity of white matter and have found no issues. I have attached a self explanatory picture. I wonder if you can help me to fix grey matter boundary errors. Thanks a lot in advance for your help! Best regards! -- Giusy Chinnici

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Pial surface missing parts of the brain
by ye tian 11 Jul '13

11 Jul '13

Dear Freesurfers, Is it true that a small piece of the brain is missing in the attached (all three views)? How do I correct this problem? Thank you very much! Sincerely, Ye

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Editing multiple sources of error in freesurfer
by ye tian 11 Jul '13

11 Jul '13

Dear freesurfers, I have a subject for which I need to delete some dura in brainmask.mgz and to add some control points. I wonder whether I can do it the following way (to save time): 1. Manually delete extra dura in brainmask.mgz 2. recon-all autoreon1 3. Add control points 4. recon-all -autoreon2-cp -autorecon3 Thank you very much! Sincerely, Ye

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Re: [Freesurfer] (no subject)
by Douglas N Greve 11 Jul '13

11 Jul '13

Hi Nick, please remember to post to the list and not to us personally. To answer your question, you could create an run an analysis with just the button press. Go into the analysis and get the button press regressor from X.mat, then save it as a text file in the run folder. Then make your analysis and specify this as a task regressor. I *think* that should work. doug On 07/11/2013 02:57 PM, Nicholas Paul Denisuk wrote: > Thanks Doug, > > This is actually a retinotopy analysis and the paradigm files are > phase encoded. Is there any possible way to regress out the activity > associated with the button presses. > > Thanks for your assistance, > > Nick > > On 7/9/13, Douglas N Greve <greve(a)nmr.mgh.harvard.edu> wrote: >> Why not include it as a condition in your paradigm file? >> doug >> >> >> On 07/09/2013 03:47 PM, Nicholas Paul Denisuk wrote: >>> Dear Freesurfer Users, >>> >>> I am trying to regress out the activity associated with button presses >>> in my GLM analysis. How do I generate a nuisance regressor file >>> analogous to a white matter regressor generated in functional >>> connectivity (a one column time course file)? >>> >>> Thanks you, >>> >>> Nick >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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. >> >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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