Freesurfer October 2008

freesurfer@nmr.mgh.harvard.edu

71 participants
110 discussions

legacy option
by R D 08 Oct '08

08 Oct '08

Hello, I have some surfaces created by freesufer in 2006. Spherical registration was not done at that time, which needs to be done. I ran recon-all with -legacy, but it crashed due to disk space problems. Now it doesn't run either with or without -legacy option. When -legacy is specified, it says "this is not a legacy analysis. It once was, but it has been fixed." Without -legacy, it asks for some files such as filled.mgz and aseg.mgz that are not present. Is there a way to 'reset' the analysis (e.g., change a flag somewhere) so it can start over with -legacy? thanks, Rutvik

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Re: [Freesurfer] volumes in wmparc.stats vs. aparc.stats
by bell0368＠umn.edu 08 Oct '08

08 Oct '08

I was wondering how the calculations of the wm volume were performed as well. The six values below are volume values from aseg I believe. I assume mris_wm_volume does more than sub-divide these regions into the wm parcellations, but probably also includes partial volume estimations along the wm/gm surface, is this correct? I basically have the same question for the gm volume values in aparc.stats; do they include partial volume calculations from the gm/pial and gm/white borders? Which binary is used to create these values for gm in aparc.stats... is it mri_segstats (with --pv)? I was assuming it would be an mris (surface) calculation as well. I am asking because if you use tkmedit to view the ?h.surface files and load the aparc+aseg or wmparc segmentation volumes in also, the surfaces and the segmentations don't seem to line up. Is there a way to create a segmentation volume that includes partial-volumed voxels at the gray/white and gray/pial boundries? Thanks for your help. Chris Bell the interior voxels are only included in the volume if they are one of the following in the aseg.mgz: case Left_Cerebral_Cortex: case Right_Cerebral_Cortex: case Left_Cerebral_White_Matter: case Right_Cerebral_White_Matter: case Left_WM_hypointensities: case Right_WM_hypointensities: cheers, Bruce On Tue, 15 Jul 2008, Marin Richardson wrote: OK, so aparc.stats is better for cortical gray matter. I want to look at the parcellated white matter volumes as well - is the only/best option to use the wm volumes from wmparc.stats? Also, when using mris_wm_volume to calculate total white matter, I saw the result defined as the volume within the white matter surface minus non-WM structures? Can you tell me which regions are and are not included? Marin Doug Greve <[EMAIL PROTECTED]> 7/15/2008 12:02 PM >>> It is better to use the aparc as it is derived from surface measurements, which have sub-voxel resolution. The wmparc.stats are generated by counting 1mm^3 voxels. doug Marin Richardson wrote: Hi all, I noticed that the gray volumes for parcellated cortical regions in wmparc.stats are different from those for the same region in aparc.stats (e.g. ctx-lh-middletemporal = 8419 in wmparc.stats, middletemporal = 9466 in lh.aparc.stats). Why are the values different and which one is a better measure to use? Thanks, Marin

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Can Optseq produced mixed blocked/event-related design?
by BumSeok Jeong 08 Oct '08

08 Oct '08

Dear Freesurfer expert, I'd like to make mixed blocked/event-related design using Optseq. (15sec fixed block - 15sec condition 1 block - fixed block - 15sec condition2 block ....) This below command does not seem to produce what I want. optseq2 --ntp 129 --tr 1.5 --tprescan -9 --psdwin -1.5 21 1.5 --nsearch 10000 --ev Condition1 3 15 --ev Condition2 3 15 --ev fix 15 6 --nkeep 2 --o test Any comment will be appreciated. thanks, Bumseok

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Coordinates in tkmedit
by Juergen Haenggi 08 Oct '08

08 Oct '08

Dear FS experts I posted another email about my confusion with the coordinates in tkmedit. When I move horizontally over the coronally presented image, the y-coordinate only change in the range of 1-2 mm. When I move vertically the y-coordinate change from 28 at the top to 8 at the bottom. Does it mean that the image is oblique oriented in the native space? Thanks Regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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qdec.table.dat error
by Mishkin Derakhshan 07 Oct '08

07 Oct '08

Hi, When I try to load a qdec.table.dat I always get the same error: sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR I've tried digging around through the archives and still can't seem to find a solution for this problem. I've tried tcsh and the bash shell. Here is a bit more information and my qdec.table.dat is attached. Any ideas on how to get qdec up and running would be very useful. thanks, mishkin FREESURFER_HOME: /lab1/FreeSurfer/4.0.5/quarantine Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.0.5 Debian version: lenny/sid Kernel info: Linux 2.6.24-18-generic x86_64 opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> qdec & opus:/lab1/FreeSurfer/4.0.5/ms-mni/testing> Reading /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/tkUtils.tcl Using /lab1/FreeSurfer/4.0.5/quarantine/lib/tcl/fsgdfPlot.tcl Loading data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat... Setting SUBJECTS_DIR to '/lab1/FreeSurfer/4.0.5/ms-mni/testing' Number of columns: 4 fsid column: 1 Number of factors: 3 Number of subjects: 2 Reading discrete factor levels from config file /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/gender.levels...'Male','Female', done. Data table /lab1/FreeSurfer/4.0.5/ms-mni/testing/qdec/qdec.table.dat loaded. SUBJECTS_DIR is '/lab1/FreeSurfer/4.0.5/ms-mni/testing' sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester' in SUBJECTS_DIR sh: Syntax error: Bad fd number ERROR: QdecProject::VerifySubjects: Couldn't find subject 'tester2' in SUBJECTS_DIR Error loading the data table.

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help with mri_segement
by Paul L Aparicio 07 Oct '08

07 Oct '08

Dear Freesurfers, I am trying to inflate a high resolution (0.5mm iso) monkey brain. I am currently at the mri_segment stage and this program just hangs on me. I am not sure why it is hanging or where I can look to figure this out? Any suggestions or help would be very appreciated! thanks paul

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Fixing pial surface for missing lateral grey matter
by John Sheppard 07 Oct '08

07 Oct '08

Hey Freesurfers, I have a question regarding segmentation in autorecon2. I have a bunch of sagittally-acquired MRI data -- Freesurfer has done a decent job after we manually added control points on the data and resegmented. The problem is that FS ends up leaving out some lateral areas of cortex. After control points, I am satisfied with the grey/white boundary but the pial surface could stand improvement. I am attaching an image to this email showing a segmentation in the coronal plane. Seems like a chunk or lateral temporal cortex is missing in the left hemi (and a little bit of missing cortex in right hemi too.) I turned the brightness up a bit so you could see the missing cortex in brainmask.mgz -- the lateral stuff as you can tell is not quite as intense as the more medial voxels, which is probably the root of the problem. First of all, I want to get a sense of what is reasonable to expect. Does this look like a reasonable segmentation or is it reasonable to try and improve this? My PI is concerned about the missing lateral GM in any case. Second, I was curious if any experienced users had advice regarding ways to get this missing cortex included in segmentation - specifically the situation in the left temporal lobe. Going off the website, since the white/grey surface looks correct, control points should not be used. (I don't know whether putting a few *right* outside the surface might help expand pial surface? I might try that more if you think it could help..) The guide would then suggest that pial surface edits must be made manually on every slice prior to re-running autorecon2-pial. This would take a long time for 1 person with 34 brains, but is certainly a possibility. Downside to this is it becomes somewhat subjective for someone with only a rudimentory understanding of neuroanatomy. What if I could run the autorecon2 workflow step-by-step and try adjusting normalization parameters? There are two normalizations here, using mri_ca_normalize (-canorm) and mri_normalize (-normalization2). mri_ca_normalize has a flag -p, that specifies percentage of likely wm to use as control points (defaulting to 50%). Bumping this up may improve intial segmentations since we've had to extensively add control points, though I suppose the end result would be about the same (in theory). mri_normalize has a number of parameters that might effect this, as well as various programs called in the segmentation process. Long story short, does anyone know of any parameter adjustment approach to this, or is manual editting of pial surface the only solution? Thanks! John Sheppard

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Anatomical question
by Tommaso De Marco 07 Oct '08

07 Oct '08

Hi all, sorry for my ignorance in anatomy, but I'm an engineer, not a physician. I would know what is the relationship in freesurfer between the gray matter and the cortical ribbon. I load in a matlab environment the ribbon.mgz file, and I see that this surrounds the white matter defined by the filled.mgz file; so I 'm thinking to use the ribbon file to find the gray matter voxels. Is there a way to build a file like the ribbon.mgz or the filled.mgz also for the gray matter, in which gray-matter points are highlighted like for the white matter points? Regards

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question mri_glmfit
by j janssen 07 Oct '08

07 Oct '08

Hi, using version 4.0.5 i ran the command: mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh --C qdec/diff-1-2.txt --glmdir stats/ it worked. then i did: mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/newperm_lh --glmdir stats/newperm_lh/ output: gdfReadHeader: reading qdec/qdec.fsgd INFO: DeMeanFlag keyword not found, DeMeaning will NOT be done. Continuous Variable Means (all subjects) 0 Age 15.4819 Class Means of each Continuous Variable 1 control 15.0882 2 patient 15.7551 INFO: gd2mtx_method is doss Reading source surface /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white reading group avg surface area 822 cm^2 from file Reading in average area /home/neuro/joost/redes/maranon/freesurfer/fsaverage/surf/lh.white.avg.area.mgh simbase stats/perm_lh Number of vertices 163842 Number of faces 327680 Total area 65416.648438 AvgVtxArea 0.399267 AvgVtxDist 0.721953 StdVtxDist 0.195470 $Id: mri_glmfit.c,v 1.138.2.1 2007/09/12 15:38:19 nicks Exp $ cwd /home/neuro/joost/redes/maranon/freesurfer cmdline mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf fsaverage lh --C qdec/diff-1-2.txt --sim perm 1000 1.3 stats/perm_lh --glmdir stats/ sysname Linux hostname fedoraneuro.lim.local machine x86_64 user neuro FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh logyflag 0 usedti 0 FSGD qdec/qdec.fsgd glmdir stats/ DoFFx 0 Loading y from /home/neuro/joost/redes/maranon/freesurfer/qdec/N83_only_boys.mgh Matrix condition is 404.504 search space = 82220 ERROR: design matrix is not orthogonal, cannot be used with permutation. If this something you really want to do, run with --perm-force mri_info N83_only_boys.mgh gives 83 frames. what´s wrong with my design matrix? thanks! -joost

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Confusion about coordinates in tkmedit
by Juergen Haenggi 07 Oct '08

07 Oct '08

Dear FS experts I loaded the aseg results in tkmedit. When I navigate over the image all three Talairach coordinates change, which does not make sense for me. Actually I expected that only two coordinates changed when moving over the image. In the volume index of the "Mouse" section, only two number change and the third number keeps at a specific value. Although I had loaded the image coronally, it is the third number that keeps at a specific value. Does the third number is not the z-coordinate? Thanks a lot for help Best regards Juergen ----------------------------------------------------------- Juergen Haenggi Ph.D. (Dr. des.) Division of Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi(a)psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) -----------------------------------------------------------

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Freesurfer October 2008