Freesurfer

freesurfer@nmr.mgh.harvard.edu

10 participants
30058 discussions

Differences between version 5.2.0 and 6.0.0
by Patrik Krumpolec 01 Feb '18

01 Feb '18

I want to ask about differences in brain segmentation with freesurfer version 5.2.0 and 6.0.0. My dicom data have original size 0.375x0.375x0.75 mm and 600, 640, 224 voxels. If I process the data vith the version 5.2.0, freesurfer conformed the data to 1 mm size and 256 voxels for all directions. In the result brain structures has volume eguals to number of voxels. But if i use version 6.0.0, there are data not conformed and in the results the volume of structure is different form number of voxels. So, now I don't know what results is correct: from the version 5.2.0 or 6.0.0 At first I think that version 6.0.0 is not good because my collegues from another institution have results with the volume eguals to number of voxels (version 5.3) but they have data with voxel size 1x1x1 mm. So, I think that it is natural that volume is eguals to number of voxels. But my data have not 1x1x1 mm voxel size. Please, Could You help me! Thank You very much! patrik krumpolec

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Average template issue in M1 region
by Dr. Konstantin Weise 01 Feb '18

01 Feb '18

Dear freesurfer-team, in my current studies, I am using the make_average_subject function to generate a group template of 14 subjects. I am doing TMS motor studies, so I am primarily interested in the region around M1. Independent on the number of subjects, I experience a meshing issue right on the gyral crown of the hand knob. There are 2-3 very large triangles. I attached an example image to this mail. I also saw this issue in the average brain you shipped with the software. Do you have any idea how I can fix that? I would be very grateful, if you could help me in this concern. The same problem occured when I generated the average template for only 3 of the 14 subjects. (freesurfer version 6.0.0) Thank you very much and best regards! Konstantin ----------------------------------------------------------- Dr.-Ing Konstantin Weise Research group "Cortical Networks and Cognitive Functions" Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A, 04103 Leipzig, Germany Phone: +49 341 9940-2418 Fax: +49 341 9940-2624 Email: kweise(a)cbs.mpg.de

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Re: [Freesurfer] annotation to volume with custom color scheme (Yeo parcellations)
by Jingwei Li 01 Feb '18

01 Feb '18

Hi Dorit, The reason why the colors look off is that mri_aparc2aseg will automatically add 1000 for left cerebral cortex and add 2000 for right cerebral cortex. Therefore, for example, a left hemisphere voxel in network 5 will have a value of 1005 in your test.mgz. Here is my suggestion: 1. Find the indices of left/right cerebral cortex by extracting the voxels with a value of 3 or 42 in the subject's aseg. 2. Use those indices to mask out the voxels that are not cerebral cortex in your test.mgz file (i.e. set non cerebral cortical voxels to be 0). 3. For the cortical voxels, you need to subtract 1000 for those between 1000 and 2000; and subtract 2000 for those greater than 2000. Best, Jingwei

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dev version
by 郑凤莲 01 Feb '18

01 Feb '18

Hi all experts, I am using freesurfer dev version for segmentation of hippocampus and amydala. I have a doubt about it. 1. In FS 6.0, I can type '203-226' in freeview for viewing subfields of hippocampus. In dev version, When I type 'freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v2x.FS60.mgz:colormap=lut', there are subfields of hippocampus and amydala. How can I view them respectively, and get corresponding colors to every subfield? 2. The hippoSFvolumes.txt shows the volume of body and head of some subfields, such as CA1, CA3. But When I type 'freeview -v nu.mgz -v lh.hippoAmygLabels-T1.v2x.FS60.mgz:colormap=lut', it seems to serve the body and head as a whole. Is there any way to resolve it? Sincerely, Zheng

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Fw: Postdoc fellowship at Merck
by Yendiki, Anastasia 31 Jan '18

31 Jan '18

A two-year postdoctoral fellowship in the Center for Observational and Real-World Evidence (CORE) division at Merck, applying quantitative methods to improve healthcare quality/outcomes and reduce cost: https://taleo.msd.com/careersection/merck_external_career_section/jobdetail…

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Yendiki Anastasia config file
by Renew Andrade 31 Jan '18

31 Jan '18

Here is the configuration file. I think is the default by tutorial.

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Issue with mri_convert on centOS 7
by Cooke,Danielle ( BIDMC - Neurology ) 31 Jan '18

31 Jan '18

Hello, I recently ran into issues using mri_convert on a CentOS 7 platform while having the same command work fine on CentOS 6. The error that results is: Segmentation fault (core dumped) I've tried on multiple machines with both operating systems to confirm the issue. I was wondering if you might have any insights or suggestions on how to fix this. Thank you! Danielle ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

2 3

Longitudinal TRACULA study
by Donatas Sederevicius 31 Jan '18

31 Jan '18

Hi, I want to clarify some aspects longitudinal TRACULA processing before processing my data. For example, I have 3 timepoints of data of the same participant: sub101_01 sub101_02 sub101_03 All of these have structural and diffusion data (same scanner, same acquisition parameters). I processed structural data using FS longitudinal pipeline and got the following: base_101 sub101_01.long.base_101 sub101_02.long.base_101 sub101_03.long.base_101 Now I want to run longitudinal TRACULA processing. If all data is OK after quality checking (struct and DWI) I could set the configuration file as follows: set subjlist = ( sub101_01 \ sub101_02 \ sub101_03 ) set baselist = ( base_101 \ base_101 \ base_101 ) It turns out that DWI data of sub101_01 is extremely distorted and cannot be used for processing. Should I re-process struct data based on the last two timepoints or is it perfectly fine to use the base and long derived from all timepoints although I’m running tracula for the last two timepoints of DWI? In addition to that, is it fine to run longitudinal TRACULA on a list of subjects where some of them have only one timepoint of data and structural processing underwent longitudinal pipeline for that one timepoint? Thank you for your answers. Best, Donatas

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annotation to volume with custom color scheme (Yeo parcellations)
by Dorit Kliemann 30 Jan '18

30 Jan '18

Hi, I’m trying to use the Yeo2011 annotations to create individual volume masks in subject space. I first use mri_surf2surf to map the annotations from fsaverage to individual subjects: mri_surf2surf --srcsubject fsaverage --trgsubject subject --hemi rh --sval-annot fsaverage/label/rh.Yeo2011_7Networks_N1000.annot --tval $SUBJECTS_DIR/subject/label/rh.Yeo2011_7Networks_N1000 Then I use mri_apar2aseg to map the annotation from the surface to the volume and thought he annot-table flag would use the labels provided in the custom color lut file. mri_aparc2aseg --s subject --o test.mgz --annot Yeo2011_7Networks_N1000 --annot-table path_to/Yeo2011_7Networks_ColorLUT.txt However the output is using different segmentation/color assignments. I can certainly find out which segmentation corresponds to which color and extract them separately (i.e. with fslmath or mri_binarize)..just wandering if I missed something or something changed since these posts? https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg35247.html Thanks Dorit

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Re: [Freesurfer] Strange Segmentation
by Antonin Skoch 30 Jan '18

30 Jan '18

Dear Arkadiy, I see sometimes these kind of errors. I think they are caused by local mis-segmentation due to WM hypointensities (enlarged perivascular spaces or other lesions, usually benign) located just under GM. Sometimes it is hard to discern where it is a hypointensity and where it is just a sulcus. I recommend to assess them using all 3 slice orientations. I correct them by editing wm.mgz (filling in voxels by value 255). Regards, Antonin Skoch Dear Experts, This brain looks a little bit strange to us, and I was wondering if someone might be able to chime in about whether this is worth editing, based on the screenshots of different slices from the sagittal view.. Thank you for your expertise. -Arkadiy

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