Freesurfer February 2010

freesurfer@nmr.mgh.harvard.edu

96 participants
153 discussions

Longitudinal processing clarification
by Derin Cobia 16 Feb '10

16 Feb '10

(Questions for all, but maybe more directed towards Martin) I have some questions about manual edits in regard to the longitudinal stream. Based on the current info on the wiki page, it appears that no edits are pushed forward from the cross-sectional (initial) runs of the subject data, as any information on the *.long.* runs come from the template. However, I've noticed that WM edits and surfs from the template are used in for the *.long.* processing. In essence, my question is when/where should manual edits (i.e., control points, WM, pial edits) occur when conducting longitudinal processing in 4.5? It seems I remember that in 4.3 edits in the cross-sectional work would be pushed forward to the *.long.* images, but such is not the case anymore (?). Are edits to occur in the template (i.e., 'base') now, or in the *.long.* runs? Thanks. -Derin

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a question about rebuild_gca_atlas.csh
by Guang Zeng 15 Feb '10

15 Feb '10

Hi, there, I am using the rebuild_gca_atlas.csh to build our own subcortical atals now, and met a problem at the second step which is # Train using ONE_SUBJECT, the command line is: mri_ca_train -prior_spacing 2 -node_spacing 8 -mask brain.mgz -parc_dir seg_edited.mgz -xform talairach_man.xfm -T1 norm.mgz -check $OneID /data1/radiology/m047599/temp_fs_2/freesurfer-v4.5.0/subjects/average/RB_12-Feb-2010.gca and it gave me errors such as; ERROR: Left_Caudate: 104 167 182, tal *** x=22.896236 > 5 ***, y=33.105412, z=-16.869007 ERROR: Left_Caudate: 104 167 183, tal *** x=22.900818 > 5 ***, y=34.053909, z=-16.893997 ERROR: Left_Caudate: 104 167 184, tal *** x=22.905401 > 5 ***, y=35.002407, z=-16.918985 ERROR: Left_Caudate: 104 167 185, tal *** x=22.909985 > 5 ***, y=35.950901, z=-16.943975 ERROR: Left_Caudate: 104 167 186, tal *** x=22.914564 > 5 ***, y=36.899403, z=-16.968966 ERROR: Left_Caudate: 104 167 187, tal *** x=22.919147 > 5 ***, y=37.847897, z=-16.993954 ERROR: Left_Caudate: 104 167 188, tal *** x=22.923729 > 5 ***, y=38.796391, z=-17.018944 Why it will have an error related to Left_Caudate? Is the FreeSurferColorLut.txt file called somewhere ? Thanks! Guang _________________________________________________________________ Hotmail: Trusted email with Microsoft’s powerful SPAM protection. http://clk.atdmt.com/GBL/go/201469226/direct/01/

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mris_ca_label: could not read surface file
by Alessandro D. Gagliardi 15 Feb '10

15 Feb '10

Dear Freesurfers, I just upgraded to the latest version of Freesurfer (leopard-i686-stable-pub-v4.5.0) and I want to rerun mris_ca_label to generate ?h.aparc.a2009s.annot files. I figured I would just run the command described at http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable, namely: mris_ca_label -aseg aseg.mgz <subjid> ?h ?h.sphere.reg $FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs label/?h.aparc.a2009s.annot but when I do so, I get the following error: mris_ca_label: could not read surface file /Users/adfgagliardi/Documents/Lab/subjects/hj/surf/?h.smoothwm for hj No such file or directory surf/?h.smoothwm does exist for hj, so I don't know why it says "No such file". I tried regenerating it using mris_smooth -n 3 -nw ?h.white ?h.smoothwm which completed without error, but mris_ca_label continues to say that it cannot read ?h.smoothwm Any help would be greatly appreciated. Alessandro D. Gagliardi Ph.D. Candidate Integrative Neuroscience Program Rutgers University Mind Brain Analysis adfgagliardi(a)gmail.com

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lobe volumes...
by Gonzalo Rojas Costa 15 Feb '10

15 Feb '10

Hi: There exist any tool that could show me the structures that differ between each hemisphere more than a given percentage (volume) ?... Sincerely, Gonzalo Rojas Costa

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lobe volumes...
by Gonzalo Rojas Costa 15 Feb '10

15 Feb '10

Hi: How can I get the volume of each lobe ?.. each hemisphere ?... Sincerely, Gonzalo Rojas Costa

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recon-all error during SubCort Seg
by Julie 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 previosly tried to attach the recon-all.log, but the file is too large (>200KB). 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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[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.

2 3

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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Freesurfer February 2010