Freesurfer

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19 participants
30088 discussions

Freeview NIH Color Map
by Blazey, Tyler 05 Mar '12

05 Mar '12

Hi, Is there any way to prevent the NIH color map in Freeview from displaying values higher than the max as black? I can only seem to find this option for the Heat color map. Thanks for any help, -Tyler ________________________________ The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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(no subject)
by Ryan 05 Mar '12

05 Mar '12

Hello all, I'm encountering a problem when I try to compare two timepoints for a particular subject. I run the command "recon-all -all -s 7107-46-tp1 -i 7107-46-1/001.mgz" and the end of the output stream where I receive errors shows the following below. Any help is greatly appreciated! painting output onto subject 7107-46-tp1. processing subject lh.EC_average... MRISread(/media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Too many levels of symbolic links mris_spherical_average: could not read surface file /media/raid/freesurfer/subjects/lh.EC_average/surf/lh.sphere.r$ Too many levels of symbolic links Linux mriserver.archlab 2.6.33.3-85.fc13.x86_64 #1 SMP Thu May 6 18:09:49 UTC 2010 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 7107-46-tp1 exited with ERRORS at Sat Feb 25 02:34:14 EST 2012 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -Ryan

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mri_vol2surf error writing to nifti volume
by Tina Jeon 05 Mar '12

05 Mar '12

Hi Freesurfers, I am trying to use projfrac 1 to threshold my newly created cortical label to include the entire cortical ribbon since only a small number of voxels are being included in my manual tracings. My input code is: mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_fs.nii.gz --out_type nifti --out ./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh I open the newly created surface with tkmedit and I get a display error (see below). Does anyone have any suggestions on how to absolve the issue? Thanks all help appreciated, Tina Jeon Graduate Student Advanced Imaging Research Center UT Southwestern Medical Center Error accessing display. Error accessing display. while executing "SetSlice $gnVolSlice [set gnVolSlice]" invoked from within ".w.fwToolBar.fwNavBar.fwCurSlice.bwInc invoke" ("uplevel" body line 1) invoked from within "uplevel #0 [list $w invoke]" (procedure "tk::ButtonUp" line 22) invoked from within "tk::ButtonUp .w.fwToolBar.fwNavBar.fwCurSlice.bwInc" (command bound to event) ________________________________ UT Southwestern Medical Center The future of medicine, today.

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controls points in 5.1
by Chris Hyatt 05 Mar '12

05 Mar '12

Bruce, You had posted that there is a 'backwards compatibility flag' regarding control points manually specified to the aseg normalization in Freesurfer version 5.1 (see your thread from 1/27/12 below). You said that Nick might know about this flag. I too had noticed very different behavior after adding control points in v5.0 and v5.1, as many more regions were tagged as white matter in v5.1 than in v5.0. Would anyone know if this flag exists and how to use it? Thanks, Chris Re: [Freesurfer] control point guidanceBruce Fischl Fri, 27 Jan 2012 11:58:38 -0800 Hi Mikeit's a bit hard to state the region of effect for the control points. Essentially we go through and label voxels as control points or not based on their intensity, intensity gradient and connectivity (that is, the must be 6-connected to other control points) then build a Voronoi diagram and each control point sets the scaling for its Voronoi triangle. Thus if you have a control point surrounded by others its region of effect is small, but one control point all by itself can have a large region of effect.Also, 5.1 applies the manually specified control points to the aseg normalization (norm.mgz), whereas older versions didn't. Not everyone is happy with this, so I think there is a backwards compatibility flag. Nick would know.Bruce

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pwd: permission denied
by Marcel Zwiers 05 Mar '12

05 Mar '12

Hi, I am new to FS and have encountered a weird problem that I do not know how to solve and did not find any earlier postings on. When I run recon-all on a file in my own home directory everything works normally: recon-all -subject BIG1026_1 -sd /home/mrphys/marzwi/test -i BIG1026_1.nii.gz -autorecon1 [..] However, if I run the same command on the same file, except that this file is now located in a directory of a colleague of mine that I certainly have full access to (+r+w+x), I immediately get a 'permission denied' error: recon-all -subject BIG1026_1 -sd /home/control/marhoo/Projects/BIG/Freesurfer_CorticalThickness -i BIG1026_1.nii.gz -autorecon1 pwd: cannot open directory `../..': Permission denied /bin/pwd: cannot open directory `../..': Permission denied mkdir: cannot create directory `/BIG1026_1': Permission denied [..] >From the error message it seems to me as if FS is trying to access the parent directory (of which I do not have full rights but only -r-w+x)? As this does not make a lot of sense to me I suspect there must be another cause and hope you have any ideas here. Cheers, Marcel -- Marcel Zwiers www.ru.nl/donders MR techniques +31-(0)24-3668495 Donders Institute for Brain, Cognition and Behaviour Centre for Cognitive Neuroimaging Radboud University Nijmegen, The Netherlands

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Create summary images
by Charlotte Bernard 05 Mar '12

05 Mar '12

Dear Freesurfer users, I would like to know if it is possible to quickly inspect subcortical structure segmentation quality on a large number of subjects. I have read a post on that topic but i am not sure I understand how to process. Could you give a command line to do that? Thanks a lot, Charlotte

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aseg segmentation problem
by Margaret Sheridan 05 Mar '12

05 Mar '12

Hi all, I know on principle the aseg is not supposed to be edited but we have a case (attached) where the segmentation is quite good (and the MPRAGE looks fine) but the hippocampus has been mislabeled as cortex. How should I go about re-assigning this label? Thanks! Margaret

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Coordinates of output files
by octavian lie 05 Mar '12

05 Mar '12

Dear All, I am using a pipeline for electrode coregistration including freesurfer for pial surface generation, run by default recon-all -all and mris_volmask with --save_distance option. The FS files ?h.dpial.ribbon.mgz are the sole FS output. They are converted in the pipeline to nii.gz files using the mri_convert with no specific flags. Question, what coordinate system is used in the converted nii.gz file: a native/scan system, FS system, talairach system (after several recon-all steps of talairach transformation), or NIFTI system? Is there a way to call a command to confirm the exact system used? Thank you, Octavian.

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Help! What does the error mean
by bowang21＠mail.ustc.edu.cn 05 Mar '12

05 Mar '12

Dear All I was just process the commands: recon-all -i /home/wb/test_data/ZWK/34810194 \ -s ZWK \ -sd /home/wb/test/ \ -all And then Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! I just want to know what does the error mean? Yours BoBO

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Output volume along with its calculated pia
by octavian lie 05 Mar '12

05 Mar '12

Dear All, I am increasingly fascinated by freesurfer. Here is a rookie issue: I use a source imaging program that is rather simple-minded in its MRI processing steps. To be able to use the inverse solution tools of that program, I need to use 2 volumes: - a head MRI to be used to electrode coregistration - a skull-stripped brain MR without cerebellum, including both the gray and white matter; the program needs to perform its own white matter extraction to generate the gray matter volume to be used as source space. - both MRs have to be subject to the same transforms, if any, and have to have the same origin and coordinate systems (like real head/brain pairs). So first, I am in the search of the "best" brain extraction possible, with as little dura included as possible. Besides trying to implement Andre's dura protocols, and editing the pial surface for brainmask.mgz, then running the rest of the recon-all steps, I need to be able to export in nii.gz format a volume having its pial surface as calculated by freesurfer. When exporting brain.finalsurfs.mgz with mri_convert, it looks that the calculated pial surface as visualized with tkmedit subjid brain.finalsurfs.mgz -surfs is ignored in the nii.gz file. When the output nii volume is imported in programs such as Bioimage Suite, I essentially see what looks like the outside (surface) brainmask.mgz volume as in tekmedit but not accounting for the calculated pial surface. How can I export brain.finalsurfs.mgz with its calculated pial surface as a nii volume? In other words, I would need a ribbon.mgz type volume to include the white matter on the inside. I suppose it comes down to adding options to the mri_convert brain.finalsurfs.mgz step after surfaces have been generated, but I would need some guidance Please advise. Octavian.

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