Freesurfer June 2010

freesurfer@nmr.mgh.harvard.edu

97 participants
138 discussions

Re: [Freesurfer] deepest zone in a sulcus
by Lena Palaniyappan 18 Jun '10

18 Jun '10

Thanks for the help, will try lh.sulc, for proxy 'depth' measure cheers On 18/06/2010 19:50, "Donna Dierker" <donna(a)brainvis.wustl.edu> wrote: > I would think lh.sulc might be better for this purpose. > > If neither works, you can try importing into Caret and using sulcal > depth. Hopefully lh.sulc will do the job. > > On 06/18/2010 08:49 AM, Lena Palaniyappan wrote: >> Hi all >> >> I am trying to determine a 'sulcal pit' - the deepest point in central >> sulcus. The lh.curv file gives curv values of all vertices, but how can I >> display the depth as a color map localised to central sulcus only? With such >> a display will I be able to identify the zone with maximum 'depth' as >> defined by lh.curv values? >> >> Cheers >> Lena >> >> >> 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. >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH

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regeneration of a aseg.stats file...
by Gonzalo Rojas Costa 18 Jun '10

18 Jun '10

Hi: I deleted the aseg.stats file by mistake (only that file)... How can I regenerate that file ?... I have the complete processing of that patient... Sincerely, Gonzalo Rojas Costa

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how to check the version of freesurfer?
by Dalwani, Manish 18 Jun '10

18 Jun '10

Sorry for this lame question but how can I check the current version of freesurfer? Regards, Manish Dalwani

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Binary gray matter mask
by Andrew Ward 18 Jun '10

18 Jun '10

Hi all, This may be a bit elementary, but I have been unable to figure it out. I would like to create a structurally defined binary gray matter mask for a series of subjects. I was under the impression that this was already done during recon-all with the creation of three files: ?h.ribbon.mgz and ribbon.mgz. I assumed that ribbon.mgz would be the average of ?h.ribbon.mgz, but upon looking at it in tksurfer it does not appear to be. Is there a way to average the ?h.ribbon.mgz files, or is this mask created somewhere else already? Thanks, Andy -- Andrew Ward Brigham and Women's Hospital (BBNG) Massachusetts General Hospital (GRU) Athinoula A. Martinos Center for Biomedical Imaging 149 13th St., Room 2689D Charlestown, MA 02129 Phone: 617-726-7461 Fax: 617-726-5760

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Registering a label from standard space to diffusion space
by mmoayedi＠uhnres.utoronto.ca 18 Jun '10

18 Jun '10

Hi everyone, I'm trying to use my results from CTA to make a label for diffusion tracking in probtrackx. Is there any way of doing this from the fsaverage (standard space) to the MNI152 (FSL standard) space? I'm hoping to not have to revert the label back to each individual subject, but rather use the one as a standard space seed in FSL. Is this appropriate? If not, then how do I project the label result onto each individual's surface? If so, how do I do it? Thanks, Massih

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Which volumes to use
by Ed Gronenschild 18 Jun '10

18 Jun '10

Hi, I tried to find out this from previous contributions but got lost. There's some confusion on which file(s) to use for segmented volumes. FreeSurfer generates the following image and text files: - aseg.mgz - aseg.stats - aparc+aseg.mgz - wmparc.mgz - wmparc.stats To my best knowledge aseg.stats contains the volumes from the structures in aseg.mgz, but corrected for partial volume effects. The volumes listed in the aseg.stats and wmparc.stats are in most cases different. Which volumes are the correct ones and to which of the image files are these referring? Ed

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Results
by Joana Braga Pereira 18 Jun '10

18 Jun '10

Dear Freesurfers, I'm a new/inexperienced user. I've just run a thickness comparison between two groups with qdec and got several differences throughout the brain. I would like to get the coordinates, mean thickness, z or t values of my results. Would someone tell me how to do this or kindly direct to the link in the manual/tutorial where this is explained? Thanks, Joana

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summary of qdec results
by Mayuresh 18 Jun '10

18 Jun '10

Hello Freesurfer authors/users, Does anyone know how to obtain a results summary of the qdec/mri_glmfit analysis similar to SPM output table style? Basically I see a bunch of significant areas in my qdec analysis, and I want to report these in a summary table for eg. coordinates at peak, t or z value, p value, area size. Thanks for any suggestions, Mayuresh

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cortical parcellations & ProbtrackX
by oxro0＠yahoo.com 18 Jun '10

18 Jun '10

Hi, I am trying to use Freesurfer parcellations as seed-, way- and endpoints for FSL's ProbtrackX and am following the suggestions here: http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_surface.html I was able to specify surface labels as seed points, but get error messages when trying to do the same with end- and waypoints: Below is the command line and the error. Any suggestions on how to do this with FS parcellations would be much appreciated! Thanks, Patricia /usr/pubsw/packages/fsl/fsl-4.0.4_RH4_64/bin/probtrackx --seedref=/space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+cbi_ep2d_diff_b1000/test6/dti_struct_brain.nii.gz -o /space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+cbi_ep2d_diff_b1000/test10/test10 -x $SUBJECTS_DIR/NY248_fmri_032510/label/lh.rostralanteriorcingulate.label --mesh=$SUBJECTS_DIR/NY248_fmri_032510/surf/lh.white.asc -l -c 0.2 -S 2000 --steplength=0.5 -P 1000 --xfm=/space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+cbi_ep2d_diff_b1000/test6/dti_struct2fa.mat --forcedir --opd -s /space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+cbi_ep2d_diff_b1000/fdt.bedpostX/merged -m /space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+cbi_ep2d_diff_b1000/fdt.bedpostX/nodif_brain_mask --dir=/space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+cbi_ep2d_diff_b1000/test10/ --stop=$SUBJECTS_DIR/NY248_fmri_032510/label/lh.bankssts.label Log directory is: /space/emc2/1/halgdev/projects/NYU/morphometry/DTI/NY248_fmri__nii_032510/09+cbi_ep2d_diff_b1000/test10/ ** ERROR (nifti_image_read): failed to find header file for '/home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.bankssts.label' ** ERROR: nifti_image_open(/home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.bankssts.label): bad header info Error: failed to open file /home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.bankssts.label ERROR: Could not open image /home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.bankssts.label Image Exception : #22 :: Failed to read volume /home/halgdev/projects/nyuproj/subjects//NY248_fmri_032510/label/lh.bankssts.label terminate called after throwing an instance of 'RBD_COMMON::BaseException' Read otherAbort

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intensity normalization fails?
by Frank Scharnowski 18 Jun '10

18 Jun '10

Dear Freesurfers, When importing a 3T MDEFT structural scan into freesurfer with 'mri_convert subjectname.nii 001.mgz', the image looks extremely dark (see attached tkmedit snapshot). The results of recon all are suboptimal, probably due to the bad intensity normalization. In SPM the structural looks just fine. Is there a way to correct for this? Many thanks for your help, frank

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Freesurfer June 2010