Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30132 discussions

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

3 4

segmentation fix question
by Natalia Bilenko 16 Jun '10

16 Jun '10

Hi all, I have a question about fixing surface segmentation errors while doing an anatomical reconstruction. When I try to fix some white matter surface errors by deleting/adding points to wm.mgz and running recon-all -autorecon-wm, they sometimes get fixed only partially or not at all. I was just wondering if there is any way to predict whether a certain volume fix is going to alter a segmentation, or if the only way to find out is to fix the volume and wait for the results of autorecon2. Thanks! Natalia

2 2

Volume to RAS transformation for electrode coordinates
by ckeller＠nmr.mgh.harvard.edu 16 Jun '10

16 Jun '10

Hi Freesurfers, This may be a very simple question but I am having some problems sorting it out and any help would be much appreciated. I am trying to coregister the pial surface (from a freesurfer reconstruction of the preoperative MRI sequence) with intracranial electrodes pulled from a postoperative CT scan. The electrode coordinate gathering from the CT and transformation to preopMR space was done in bioimage suite already. I believe the problem is that there is a transformation needed from voxel space to surface RAS coordinates in order to plot the pial surface in the same space as the electrodes. As of now I am plotting the pial surface with read_surf and tripatch commands in matlab. Does anyone know where I can find this transformation matrix or how to construct it? Thanks in advance. Best, Corey

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transversetemporal data is missing in rh.aparc.stats
by Guang Zeng 16 Jun '10

16 Jun '10

Hi, there, I have a subject which is processed through FreeSurfer longitudinal stream, and I found that in the rh.aparc.stats file, the data of transversetemporal is not included. So, when FreeSurfer can not detect a ROI, it will not write it into ?h.aparc.stats ? Thanks! Guang _________________________________________________________________ The New Busy is not the too busy. Combine all your e-mail accounts with Hotmail. http://www.windowslive.com/campaign/thenewbusy?tile=multiaccount&ocid=PID28…

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