Freesurfer September 2011

freesurfer@nmr.mgh.harvard.edu

119 participants
181 discussions

using mri_label2label with full path
by Chris 15 Sep '11

15 Sep '11

I have a tricky situation where we can't use symbolic links ( cifs/smb mounts ) and it doesn't make sense to copy the fsaverage to the SUBJECTS_DIR. The subjects_dir is actually a separate directory for every subject when trying to run things through the connectome toolkit. I've edited my own version of recon-all in attempts of passing full paths to some of the tools if necessary. I'm getting caught in the mri_label2label step, since its using "--srcsubject" and "--srclabel" Passing a full path to "--srcsubject" doesn't work as expected, since its assuming the path of --srcsubject exists inside my SUBJECTS_DIR. If i only pass the default "fsaverage", then that also doesn't work because it doesn't exist inside my SUBJECTS_DIR either. Any suggestions? -Chris [petty@node61 free]$ mri_label2label --srcsubject /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage --srclabel /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/label/lh.BA1.label --trgsubject test20090520_36099 --trglabel ./lh.BA1.label --hemi lh --regmethod surface srclabel = /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/label/lh.BA1.label srcsubject = /usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage trgsubject = test20090520_36099 trglabel = ./lh.BA1.label regmethod = surface srchemi = lh trghemi = lh trgsurface = white srcsurfreg = sphere.reg trgsurfreg = sphere.reg usehash = 1 Use ProjAbs = 0, 0 Use ProjFrac = 0, 0 DoPaint 0 SUBJECTS_DIR /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free/ FREESURFER_HOME /usr/local/packages/freesurfer_v5.1.0 Loading source label. Found 4129 points in source label. Starting surface-based mapping Reading source registration /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free///usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/surf/lh.sphere.reg MRISread(/mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_tes…: could not open file No such file or directory ERROR: could not read /mnt/BIAC/munin2.dhe.duke.edu/BIAC/TestSuite.01/Analysis/speed_test/20090520_36099/free///usr/local/packages/freesurfer_v5.1.0/subjects/fsaverage/surf/lh.sphere.reg

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FSGD Contrast Setup Question
by Adam Nitenson 15 Sep '11

15 Sep '11

Hi Freesurfers, I am trying to set up both a 2 Group 1 Covariate and a 4 Group 1 Covariate analysis but just want to make sure I'm using the correct contrast option. For the first analyis, the two groups are Drug Pre and Drug Post, with folate-serum level as a covaraite. We want to keep the covariate under consideration in our analyses, but we really want to look at the difference between the Drug Pre and Drug Post activation (so folate-serum level is more of a nuisance variable). It seems that the first option under the 2G1V Page "Null Hypothesis: is there a difference between the group intercepts? Is there a difference between groups regressing out the effect of age? 1 -1 0 0" reflects this idea best. For the second analysis, the 4 Groups are Drug Pre, Drug Post, Placebo Pre, and Placebo Post, with the same folate-serum level covariate. We are intersted in the double subtraction of (Drug Post - Drug Pre) MINUS (Placebo Post - Placebo Pre), but again wish to covary by folate level. For this it seems like contast 7 on the 4G1V page "is there an interaction between gender and handedness regressing out the effects of age? 0.5 -0.5 -0.5 0.5 0 0 0 0" is best. Is this the best way to go about analyzing these two questions? Thanks, Adam Nitenson, B.S. Brain Genomics Lab Massachusetts General Hospital nitenson(a)nmr.mgh.harvard.edu Phone: 617-643-3215

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mri_mcsim and mri_glmfit-sim
by MCLAREN, Donald 14 Sep '11

14 Sep '11

I am trying to figure out how to cluster some data on the cortical surface; however, I've run into a few issues: (1) I can't seem to find a description or examples for running mri_mcsim and mri_glmfit-sim won't work because I'm not using FSFAST to create my statistical maps. (2) A previous email suggested that there are stored values that I could lookup, but I can't seem to locate the files anywhere. (3) With respect to the fwhm values used in the simulations, it was suggested that this be matched to the fwhm.dat file output from mri_glmfit; however, since I didn't use mri_glmfit, I don't have fwhm.data file. Should I just use the smoothing used on the surfaces? Any thoughts would be appreciated. Best Regards, Donald McLaren ================= D.G. McLaren, Ph.D. Postdoctoral Research Fellow, GRECC, Bedford VA Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Office: (773) 406-2464 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email.

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Converting a cluster to a ROI without manually drawing
by Nasim Maleki 14 Sep '11

14 Sep '11

Hi all, In qdec, is there a way to convert a cluster to an ROI without manually drawing the ROI? I'm talking about selecting clusters on the mc-z maps. Thanks, Nasim

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statical question recon-all -qcache -s (subject) ?
by Knut J Bjuland 14 Sep '11

14 Sep '11

Hi Can I use a different version of Freesurfer to run recon-all -qcache -s (subject) than the version used for recon-all -all -s (subject)? Knut J

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.img extension read as analyze even though hdr says nifti1
by Satrajit Ghosh 14 Sep '11

14 Sep '11

hi all, when a .img extension file is passed to freesurfer routines, it is read in as analyze even if the header says it's a nifti image. we have observed that this causes a left-right flip in some cases. since a .img cannot exist without a header to be meaningful, shouldn't the appropriate type be detected from the header? also it would be good to know if this behavior is consistent across all of freesurfer or restricted to certain binaries. see below for mri_info output cheers, satra $ mri_info con_0001.img Volume information for con_0001.img type: analyze4d dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.0000 0.0000 0.0000 78.0000 0.0000 2.0000 0.0000 -112.0000 0.0000 0.0000 2.0000 -50.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -8 ras to voxel transform: -0.5000 0.0000 0.0000 39.0000 -0.0000 0.5000 -0.0000 56.0000 -0.0000 -0.0000 0.5000 25.0000 0.0000 0.0000 0.0000 1.0000 $ mri_info con_0001.hdr Volume information for con_0001.hdr type: nifti1 dimensions: 79 x 95 x 68 voxel sizes: 2.0000, 2.0000, 2.0000 type: FLOAT (3) fov: 79.000 dof: 0 xstart: -39.5, xend: 39.5 ystart: -47.5, yend: 47.5 zstart: -34.0, zend: 34.0 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = -1.0000 : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = -17.0000 : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = 18.0000 Orientation : LAS Primary Slice Direction: axial voxel to ras transform: -2.0000 0.0000 0.0000 78.0000 0.0000 2.0000 0.0000 -112.0000 0.0000 0.0000 2.0000 -50.0000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -8 ras to voxel transform: -0.5000 0.0000 0.0000 39.0000 -0.0000 0.5000 -0.0000 56.0000 -0.0000 -0.0000 0.5000 25.0000 0.0000 0.0000 0.0000 1.0000

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flipped orientation in tksurfer and tkmedit
by Ilana Hairston 14 Sep '11

14 Sep '11

Hi there, We recently had a problem that tksurfer and tkmedit were flipped relative to each other. Basically, when saving a point in the left hemisphere in tksurfer it it loaded in the right hemisphere in tkmedit. Any ideas how this could have happened? Thanks ilana -- ****************************** Ilana Hairston ,PhD Research Assistant Professor 4250 Plymouth Rd. (rm 2439) Psychiatry Department, Addiction Research Center University of Michigan, Ann Arbor MI 48109-2700 Tel: 734-232-0232; Mobile: 650-906-8449 ******************** Reminder: Women do 66% of the work worldwide, earn 10% of the income, and own 1% of the world's property

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mean and stdev group-wise
by Tetiana Dadakova 14 Sep '11

14 Sep '11

Dear list, I would like to calculate mean and stdev of thickness group-wise. Could you please give me a hint how to do it? Thank you, Tanja.

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tksurfer sliver problem
by Michael Harms 14 Sep '11

14 Sep '11

Hi guys, So, the infamous tksurfer "sliver" display problem has reared its ugly head on some of the systems that I'm accessing, but in a manner that I can't make any sense of across the systems. Machine 1: CentOS 5.5, 64 bit, FS versions 4.5.0 and 5.0.0 installed Sliver problem is present for v4.5.0, but not 5.0.0 Machine 2: RHEL Server 5.7, 64 bit, FS versions 4.5.0, 5.0.0, and 5.1.0 installed. Sliver problem is present for all 3 FS versions. For both machines, I'm viewing the results in a VNC server, and 'glxgears' works fine in each. The results of 'glxinfo' in a terminal within the VNC Server on each machine indicates that the same rendering is being used on each. i.e,. direct rendering: No OpenGL renderer string: Mesa GLX Indirect OpenGL version string: 1.2 (1.5 Mesa 6.5.1) What I find particularly puzzling is that tksurfer works fine on FS v5.0.0 on Machine 1, but not FS 4.5.0 on the same machine. Yet the sliver problem is present for v5.0.0 on Machine 2, indicating that it isn't simply an FS version issue either. I was wondering if the above behavior makes sense to someone, so that I can have something more concrete to take to the admins of each system. thanks, -MH -- Michael Harms, Ph.D. -------------------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 Renard Hospital, Room 6604 Tel: 314-747-6173 660 South Euclid Ave. Fax: 314-747-2182 St. Louis, MO 63110 Email: mharms(a)wustl.edu --------------------------------------------------------------------

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Re: [Freesurfer] Reference
by Louis Nicholas Vinke 14 Sep '11

14 Sep '11

Hi, On the pages below there are some links to articles describing how the FS cortical and sub-cortical atlases were created. https://surfer.nmr.mgh.harvard.edu/fswiki/SubcorticalSegmentation https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation -Louis On Wed, 14 Sep 2011, Anne Bailey wrote: > Hi, > > > I am a PhD student currently using Freesurfer for analyses and I was > wondering if you could provide me with the reference for the original brains > that were used as the basis for the automatic parcellation of cortical and > subcortical structures. > > If I have contacted the wrong person, could you please forward my inquiry to > someone who can point me to this information? > > Thank you! > > Anne Bailey > >

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Freesurfer September 2011