Freesurfer June 2016

freesurfer@nmr.mgh.harvard.edu

152 participants
213 discussions

BERT is not working correctly with the toolbox list below the brain
by John Mitchell 10 Jun '16

10 Jun '16

When I open freesurfer and type the command to pull up bert the brain pops up but the toolbox (icons) below it that are supposed to come up as well do not? Help is appreciated!

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Freesurfer Help
by John Mitchell 10 Jun '16

10 Jun '16

Hello, I just downloaded and installed Freesurfer and I had just a few basic questions. 1. When I type in the command to "test the installation type" using "tksurfer bert lh inflated -annotation aparc" I get the bert brain image, however I don't get the tksurfer tools popup below it with all the different icons and options and I don't know why?2. When I go to the GIMP image editor just to explore and play around with it, I selected the paint brush to draw on my selected image, however when I go to change the color from black to any other color (and it shows that I've selected a different color) it still draws/paints black on my image? Thank you for time and help!-John M.

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Re: [Freesurfer] using both T1/T2 and resolutions
by Matt Glasser 10 Jun '16

10 Jun '16

Hi Jim, I would just use the HCP Pipelines for that: https://github.com/Washington-University/Pipelines, as they take care of all of those things re FreeSurfer. I would set to using the 0.8mm templates so that nothing is down sampled. Peace, Matt. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Alexopoulos, Dimitrios" <Alexopoulos_D(a)kids.wustl.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, June 10, 2016 at 10:56 AM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] using both T1/T2 and resolutions Hi, We¹d like to process pediatric data through the complete FS 5.3 pipeline. The T1/T2 data are acquired with a 3T Siemens as follows: T1 mpr sag - 0.82x0.82x0.85 T2 Space - 1x1x1 We¹d like to process using both the T1 and T2 (for better dura removal and possible myelin analysis). Is it possible to use the hires T1 and have data not downsampled to 1x1x1? Ifpossible, can this be done in tandem with the lower resolution T2-space? What recon-all command would be best for this process? Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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Brainstem Substructures does not work.
by shi yao wang 10 Jun '16

10 Jun '16

Dear FSL expert: Firstly, I would like to thank for the reply from Douglas. Thank you for your suggestion! aparcstats2table is working!. Then, I have another question about the brainstem substructures. According to the guideline, https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime I download the environment and successfully installed. However, when I running command " recon-all -s subject -brainstem-structures" it shows wrong message "ERROR: Flag -brainstem-structures unrecognized. -s 201 -brainstem-structures" So how can I fix it? Is that due to FSL version problem? If yes, how can I update to freesurfer 6.0? thanks! Lawrence Emory.

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using both T1/T2 and resolutions
by Alexopoulos, Dimitrios 10 Jun '16

10 Jun '16

Hi, We'd like to process pediatric data through the complete FS 5.3 pipeline. The T1/T2 data are acquired with a 3T Siemens as follows: T1 mpr sag - 0.82x0.82x0.85 T2 Space - 1x1x1 We'd like to process using both the T1 and T2 (for better dura removal and possible myelin analysis). Is it possible to use the hires T1 and have data not downsampled to 1x1x1? Ifpossible, can this be done in tandem with the lower resolution T2-space? What recon-all command would be best for this process? Jim The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution 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 email.

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Symmetric label on fsaverage
by Alexandre Routier 10 Jun '16

10 Jun '16

Hello everyone, We used tksurfer to draw a specific region on the left hemisphere of fsaverage subject and we would like to automatically register the label from the left hemisphere to the right hemisphere. Since FreeSurfer provides tools to compute a symmetric fsaverage ( https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi) I was wondering if there was any command to have the manually drawn label on the left hemisphere to the right hemisphere. Thanks in advance for your help. Alexandre

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Coordinate system in mris_convert
by Alexandre Routier 09 Jun '16

09 Jun '16

Hello, I would like to work with mesh representation of pial and white surfaces in vtk format. To do that, I use the following syntax: mris_convert lh.pial lh.pial.vtk However, there is a small issue after conversion: the vector called 'c_ras' (the RAS at the 'center' of the volume according to mri_info) is not taken into account. I can manually add this c_ras vector to correct that but I was wondering if there was any flag for mris_convert or a special command to do that ? This kind of flag exists for mri_tesselate (with -n flag which ables to "save surface with real RAS coordinates where c_(r,a,s) != 0") so I was hoping the same kind of flags for mris_convert. Thanks in advance for your answer ! Alexandre

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wm.mgz edits amygdala hippocampus cerebral cortex
by marco mcsweeney 09 Jun '16

09 Jun '16

Dear all Freesurfer users, I have a few questions regarding wm.mgz edits. I am very new to this area and have only recently started using Freesurfer so please excuse me if my questions appear naive or misinformed. I have managed to make most of the necessary edits needed to fix skullstrip errors, intensity normalization errors and pial errors, but I am a bit stuck when it comes to fixing topological defects. My question relates to what should or should not be included in the wm.mgz. Apart from the optic chiasm, which I have removed, is it normal to have, what appear to be, multiple specs included in the wm.mgz which when the aseg is loaded turn out to be parts of the amygdala and hippocampus. When I view the smoothwm.nofix these appear as jagged shard like shapes protruding out from the surface. In one publication I saw recently it was suggested that these should be removed but should this be done if they are parts of the amygdala and hippocampus. I am worried about this as these are the 2 main subcortical areas I will be focusing on. Also, is it normal for the wm.mgz to include parts of the cerebral cortex (labelled as such in the aseg). Also, most of the scans I am working with have numerous holes and handles and this is taking a very long time to fix. I have tried to run the automatic topology fixer again. This has helped a bit but the scans still require a lot of edits. Could this be down to the quality of the scans or could it be that I have edited too much - control points for example. I have followed the advice given and have tried not to make too many edits, but having said that it has taken me a very long time. Any advice in relation to any of these questions would be very very very much appreciated. Best wishes fuzzy

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Resampling the parametric map of brain activations onto a surface
by Zhao, Yue 09 Jun '16

09 Jun '16

Hi All, I am using a Ubuntu FreeSurfer v5.3.0 in the VirtualBox. I am trying to overlay a parametric map onto a FreeSurfer surface. Here are the tutorial codes I found: 1. To resample the paramatric map onto the individual's surface: mri_vol2surf --src spm001.img --srcreg register.dat --hemi lh --projfrac 0.5 --out ./spm001-lh.w --out_type paint 2. Visualize and overlay: qsurfer -stat spm001 -hemi lh -subject bert-brf 3. Configure the image by selecting "View -> Configure -> Overlay" and play with the histogram The image looks like this: [https://mail.google.com/mail/u/0/?ui=2&ik=fffa1c9b37&view=fimg&th=1552b8aa0…] I assigned one single value to the voxels in each cortical parcellation. So the white matter and subcortical regions (e.g. caudate, putamen, hippocampus) are 0. The contrast represents the variations of the parameter across the cortex. Everything looks good to me except that I couldn't get rid of that green "noise" appearing at the hippocampus and occipital area. Does anyone have any idea why this is happening and how to get rid of it? Another minor issue is that even though I play with the histogram in "Overlay" to get the best contrast, the colorbar looks less dynamic. Too much red but very little yellow. Any suggestion to improve that? Thanks a lot! Best, Yue

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mri_binarize --rmax option unknown
by Lakhani, Bimal 09 Jun '16

09 Jun '16

Good afternoon, I am trying to run a fairly simple mri_binarize command on FS v 5.3, Linux 64bit, but when I use the option — rmax, I am getting an error that says the —rmax option is not recognized. It is made weirded because —rmin works perfectly. Here is the command line and the following error: boydsrv01:~/Desktop/Arrowsmith/Freesurfer/Output> mri_binarize --i '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07_MWF2Brain.mgz' --rmax 1.95 --o '/home/boydadmin/Desktop/Arrowsmith/Freesurfer/Output/Scan1/R07__MWF2Brain.bin.mgz’ ERROR: Option --rmax unknown Thanks very much! Bimal

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Freesurfer June 2016