Freesurfer

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30132 discussions

[Fwd: Re: Problems with tksurfer display on laptop]
by jentis＠nmr.mgh.harvard.edu 15 Feb '10

15 Feb '10

Hi, Sorry to resend this email, but I tried all the solutions listed on the help page but they don't work. My graphics card is an Intel Mobile 4 Series Chipset Integrated Graphics Controller. How do I update the drivers? Jon > have you tried updating your video drivers? Freeview doesn't currently > have any tools for tracing on the surface, I don't think. > > Bruce > On Thu, 11 Feb > 2010 jentis(a)nmr.mgh.harvard.edu wrote: > >> Hi, >> >> I have a laptop equipped with Centos and Freesurfer but I can't get >> tksurfer to properly display the surface files of either the fsaverage >> brain or individual subjects. The surfaces are either small portions >> of cortex or an assemblage of lines/dots. I have attached a few tiff >> files as examples. Is there something I can do to fix this? I have >> tried using freeview instead, and the surfaces do display properly, but >> the program does not seem to allow me to trace label files. Is there >> another way around this? Does a newer version of freeview include >> tracing ability? >> >> >> Thanks, >> Jon > > >

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Subcortical Volume Calculation
by Hui J Yu 15 Feb '10

15 Feb '10

Dear Freesurfer users, I am wondering how are the volumes calculated from stats such aseg.stat. When I export the aseg and do a voxel count and multiple the volume per voxel, my total volume is different from that is given by the stats. For example, the hippocampal volume given by aseg.stats for one of my controls is 4000 cm3, but when I export the aseg.mgz into matlab and do a voxel count (my original voxel volume is 1mm3 isotropic) for that labeled mask, the total volume is aorund 3000 cm3. Does freesurfer does some sort of intensity normalization or partial volume correction? Even if so, the magnitude of difference is large that I am puzzled. Thank you very much.

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recon-all error during SubCort Seg
by Julie E McEntee 15 Feb '10

15 Feb '10

Hello, The initial command to recon-all: recon-all -i $FREESURFER_HOME/subjects/PPG1156/1156MPRage.nii.gz -autorecon1 -autorecon2 -subjid MGZ exited with errors during SubCort Seg. At this point, I am attempting to obtain subcortical segmentation only (aseg.mgz, wm.mgz, aseg.stats), but would like to eventually run entire recon. I have attached the recon-all.log. I checked the tal transform and skullstrip- both looked OK. The scan is of a subject with Huntington's Disease so the ventricles are a bit enlarged and there is significant asymmetrical atrophy such that at least one area of brainmask.mgz was labeled as 57 (Right-Lesion). Also, there seems to be intensity variations (artifact?) A-P across cortex on slices around mid-line in sagittal view. Any ideas? Please let me know if you'd like me to upload any/all files. Thank you for your help, Julie Julie E. McEntee, M.A., C.C.R.P. Senior Research Program Coordinator Department of Psychiatry- Neuroimaging Johns Hopkins University School of Medicine 600 N. Wolfe St./ Phipps 300 Baltimore, MD 21287 Phone: 410-502-0468 Fax: 410-614-3676

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ETA on next version of FS?
by Mira Michelle Raman 13 Feb '10

13 Feb '10

Hi, We are about to start processing data from several projects using FreeSurfer, and I wanted to find out if the next version is coming out in the near future. I know Nick had asked if anyone wanted Tiger builds about a month ago, which has me thinking a new version is on the horizon, and if so will it work with Snow Leopard? Thanks, Mira Mira Michelle Raman Center for Interdisciplinary Brain Sciences Research Stanford University

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recon-all: different results on different systems
by Andreas Berger 13 Feb '10

13 Feb '10

Hi Freesurfers, we have FreeSurfer running on 10 computers: 7 computers with suse 10 32bit, freesurfer 4.5.0 32bit 3 computers with debian 5 64bit, freesurfer 4.5.0 64bit recon-all -all -i finished on all of them without any errors, so i assumed the best. out of curiousity i processed one of the subjects on both systems, and checking the results in tkmedit and tksurfer i noticed that they are visibly different. (thus in this case one of the surfaces does not look quite ok, other subjects processed on that system look fine however, i haven't looked through all of them yet). screenshots attached. also, i just started recon-all -all -s bert on both systems, so i can compare them to the original bert. what could be the reason for this failure at reproducibility? -- Andreas Berger <andreas.berger.01(a)gmail.com>

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Measuring Cortical Volume
by Jeff Sadino 13 Feb '10

13 Feb '10

Hello, I want to measure the volume of my groups' cortex, n=139, mostly males. I am using fs 3.0.5. >From the aseg.stats file, lh + rh white matter is 548,000 and gray matter is 487,000, for a ratio of 1.1. I know the aseg.stats file is not a good place to go for gray matter volume, as it is usually underestimated. Looking in the aparc.a2005.stats file, the average white matter is 606,000 and gray matter is 463,000, for a ratio of 1.3. I was surprised the gray matter actually went down, and the ratio of 1.3 seems a bit high. Is this normal? I see in the aseg.stats file, skin left over after the watershed is counted as cortex and so is a fair amount around the cerebellum. Could partial volumeing also be a possible explanation? I would think that the aparc file would be most accurate, but with these results, I wanted to doublecheck. Thanks Bruce for answering my earlier question. I am still looking at the pallidum differences and will let you know soon. Thanks! Jeff Sadino

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Segmentation fault wmparc a2009s
by Lena Palaniyappan 12 Feb '10

12 Feb '10

I am trying to derive wmparc volumes for a2009s which are by default not available in wmparc (segments read empty) _ is this because Desikan/Killiany atlas is used in wmparc by default? So I decided to run Mri_aparc2aseg for each subject using mri_aparc2aseg --s <subjid> --annot aparc.a2009s --o mri/wmparc.a2009.mgz --labelwm --rip-unknown --ctxseg aparc.a2009s+aseg.mgz I thought this would generate a new wmparc which will now include labels for wm from a2009s Then I ran mri_segstats --seg mri/wmparc.a2009.mgz --sum stats/wmparc.a2009.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject MPRAGE04 --surf-wm-vol --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt Hoping that this would allow me to obtain statistics from this wmparc file But for some reason I am getting segmentation fault message as below atlas_icv (eTIV) = 1663710 mm^3 (det: 1.170940 ) Loading mri/wmparc.a2009.mgz Getting Cerebral WM volumes from surface lh white matter volume 277542 rh white matter volume 284002 Loading mri/norm.mgz Loading mri/norm.mgz Loading mri/brainmask.mgz # nbrainmaskvoxels 1740943 # brainmaskvolume 1740943.0 # nbrainsegvoxels 260991 # brainsegvolume 260991.0 Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1190 segmentations Computing statistics for each segmentation 1 1 Left-Cerebral-Exterior 0 2 2 Left-Cerebral-White-Matter 0 3 3 Left-Cerebral-Cortex 0 4 4 Left-Lateral-Ventricle 3953 3953 5 5 Left-Inf-Lat-Vent 142 142 6 6 Left-Cerebellum-Exterior 0 7 7 Left-Cerebellum-White-Matter 15484 15484 8 8 Left-Cerebellum-Cortex Segmentation fault Could anyone help please? Cheers 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 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.

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comparison between three MRI exams of same patient...
by Gonzalo Rojas 12 Feb '10

12 Feb '10

Hi: I have three MRIs of the same patient taken at different dates/years... I need to compare the hippocampus volume (for example) between the three MRI... I want to compare also the cortical thickness between the three MRI... How can I do such computation ?... Sincerely, Gonzalo Rojas Costa Department of Radiology Las Condes Clinic Santiago Chile

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execute a freesurfer command at a specificed time/day...
by Gonzalo Rojas 12 Feb '10

12 Feb '10

Hi: How can I execute a freesurfer command at a specificed time/day ?... Any Ubuntu trick ?... Sincerely, -- Gonzalo Rojas Costa Advanced Medical Image Processing Laboratory Department of Radiology Las Condes Clinic Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Cortical thickness in controls
by Rajagopalan, Venkateswaran 12 Feb '10

12 Feb '10

Hello All, I would like to clarify the following.I couldn't find the answers i was looking for in the archives so here are my questions; 1) In some of our subjects the WM/GM interface is identified correctly but the pial surface falls short of some voxels which i want to manually edit them inorder to include them. Is there a way to only edit the pial surface if so kindly give directions or direct me the documentation page. 2) I would like to check the cortical thickness values measured in our control subjects with any already published or documented control values inorder to make sure that i am doing right. 3) In some our of subjects WM is not filled completely i.e. in filled.mgz volume there are still some ventricle regions that need to be manually filled, i have done the manual editing it there a way to run rest of the steps from this step i.e inflation smoothing etc. Now i am doing them one by one which is time consuming. Thanks in advance. Regards venkateswaran =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

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