Freesurfer

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30132 discussions

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

2 1

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.

3 2

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

2 1

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.

2 1

save custom made path on surface as label
by Erhan Genc 05 Mar '12

05 Mar '12

Dear freesurfer experts, I draw a path with the tksurfer tools on a surface, but was not able to save this path as a label. During the custom fill step it marked the whole surface and not just the path. I think it is because the path is not closed. Is there still a way to get a path as a label file? cheers, erhan -- Dipl. Psych. Erhan Genc Max Planck Institute for Brain Research Department of Neurophysiology Deutschordenstr. 46 60528 Frankfurt am Main -GERMANY- phone: +49 (69) 96769-471 fax: +49 (69) 96769-327 e-mail: genc(a)mpih-frankfurt.mpg.de http://www.brain.mpg.de/research/singer-emeritus-department/people/erhan-ge…

1 0

Changing the settings in TkMedit .tcl file
by Stephen Politzer-Ahles 03 Mar '12

03 Mar '12

Hello, I am trying to change some default settings in TkMedit by specifying my own .tcl file (using the *-tcl* flag when I call *tkmedit*), and I'm finding that some of the changes work and some do not. Here is my tcl: SetBrushShape 10 0 1 > SetTool 2 > SetDisplayConfig 2 2 0 > I got those settings from surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditReference/TkMeditScri…. I saved that in a file called tkmedit_defaults.tcl, and when I open TkMedit I call tkmedit <subject> T1.mgz -tcl $FREESURFER_HOME/tktools/tkmedit_defaults.tcl . When TkMedit opens, the tool has been set to Edit Voxels like I hoped, and the brush has been set to Circle with a radius 10 like I hoped. But it's not set to 3d (which I thought the "1" in SetBrushShape 10 0 1 would do), nor is it set to a 2x2 display from SetDisplayConfig. Does anyone have any guesses what might be causing those commands not to work? The version of freesurfer I'm using is freesurfer-x86_65-redhat-linux-gnu-stable5-20110522, which I believe is more or less the newest version. Thank you, Steve Politzer-Ahles

1 0

improve aparc+aseg result
by Ping-Hong Yeh 03 Mar '12

03 Mar '12

Hi, Our data do no get good parcellation and segmenation, mainly in the subsulcal and subcortical regions (see the attached examples), which are likely due to imhomogeneity bias and/or brain lesion. Adding control points and WM matter edits do not seem to help. Any suggestion in improving? Thank you, Ping

2 1

mri_glmfit problem with y option
by Charlotte Bernard 02 Mar '12

02 Mar '12

Dear Freesurfer users, I have tried to run mri-glmfit but I have obtained the error message: ERROR: Option --y unknown I don't understand why! I have run that command line: mri_glmfit \ --y lh.test.thickness.10.mgh \ --fsgd test.fsgd dods\ --C group.diff.mtx \ --surf fsaverage lh \ --cortex \ --glmdir test.glmdir Could somebody help me? Thanks for all, Charlotte

3 2

Postdoc fMRI Reaching and Grasping, Center for Mind/ Brain Sciences, Italy
by angelika lingnau 02 Mar '12

02 Mar '12

*Postdoc fMRI of Reaching and Grasping, Center for Mind/Brain Sciences, University of Trento, Italy* At the Center for Mind/ Brain Sciences (CIMeC), University of Trento, there is soon going to be an opening for a Postdoctoral Fellowship to work with Dr. Angelika Lingnau (http://www.unitn.it/en/cimec/11702/angelika-lingnau) in collaboration with Prof. Raffaella Rumiati, SISSA. In this project, we will use fMRI to study the effects of parietal and premotor lesions on reaching and grasping movements. *Start date:* as soon as possible *Requirements: * PhD in related field Experience with fMRI design and analysis Programming skills (Matlab or C) The Center offers an international and vibrant research setting with access to state-of-the-art neuroimaging methodologies, including a research-only 4T MRI scanner, MEG, EEG and TMS, as well as behavioral, eye tracking and motion tracking laboratories. The University of Trento is ranked first among research universities in Italy. English is the official language of the CIMeC, where a large proportion of the faculty, post-docs and students come from a wide range of countries outside of Italy. For informal inquiries, please contact Angelika Lingnau ( angelika.lingnau(a)gmail.com <angelika.lingnau(a)unitn.it>).

1 0

Data check
by Charlotte Bernard 02 Mar '12

02 Mar '12

Dear Freesurfer users, I would like to know what is the procedure to check the quality of the Freesurfer process on my subjects. I have more than 500 subjects. 1/ Have I to check each segmented region on by one for each subject? 2/ How can we check the quality of the surf process? Thanks a lot for your help, Charlotte

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