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Re: [Freesurfer] the pial and wm are larger than the inflated (beyond the inflated image)
by xi star 02 Jan '19

02 Jan '19

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the pial and wm are larger than the inflated (beyond the inflated image)
by xi star 02 Jan '19

02 Jan '19

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voxel cordinates
by Sadia Sheikh 02 Jan '19

02 Jan '19

External Email - Use Caution Dear Freesurfer experts I am using freesurfer version 6.0. I have extracted ROI's from the aseg.mgz file. Now is it possible to get the cordinates of each voxel for a particular ROI? Thanks in advance Regards Research student

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map parcellations into DWI space?
by Yerong Li 31 Dec '18

31 Dec '18

External Email - Use Caution Dear FreeSurfer experts: I am trying to map ./mri/aparc.a2009s+aseg.mgz and ./mri/aparc+aseg.mgz into DTI file. Let's say, we have a DTI file with its b-vectors: ./bvals ./bvecs ./data.nii.gz I am trying to use the command from this webpage: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat So I used the command : mri_label2vol --seg aparc+aseg.mgz --temp ./data.nii.gz --o dk-in-rawavg.mgz --regheader aparc+aseg.mgz The output file seems not very reasonable. Could you help me with this? Yerong ================================== Can you be more specific about which files you want to map into your DWI space? Eg, if you want to map wmparc.mgz, then use mri_label2vol. You will need a registration file which you can obtain with bbregister On 12/05/2018 02:34 AM, Maedeh Khalilian wrote: [Hide Quoted Text] External Email - Use Caution Dear FreeSurfer experts, I have a parcellation and a whole brain white matter files which are the outputs of FreeSurfer. I want to register them to my DWI. I mean I want my parcellation and white matter to be in the physical space of my DWI. Can FreeSurfer do it for me? If not , can you suggest me a toolbox that can do it fast? I would be grateful if u could help me. Cheers, Maedeh,

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plotting mean T1/T2 values in the different cortical layers
by Anik Dar 31 Dec '18

31 Dec '18

External Email - Use Caution Hi All, I have created cortical surfaces corresponding to 25%, 50%, 75% of the cortex. Now I want to plot the T1/T2 values corresponding to these different layers.I believe I have to use mri_vol2surf. What options in the mri_vol2surf do I need to use to create these T1/T2 maps corresponding to these different layers of the cortex ? Please let me know. Merry christmas and a happy New Year. Thank you, Ani

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Notebook specification
by mustafa amin 30 Dec '18

30 Dec '18

External Email - Use Caution Dear Freesurfer Members, First I would like to introduce myself my name is Mustafa Amin, and I’m planning to do a study to measure the volume of prefrontal cortex, hippocampus, and ventricle of patients with schizophrenia comparing them with control in Medan Indonesia. I read and saw information that freesurfer is capable in doing the measurement, however I am still not sure about what kind of notebook specification that I need to download and install it. For my knowledge, this is the first study that will be done in Indonesia so every explanation and further information about freesurfer and the notebook will make me very grateful. I’m thinking to buy an I5 intel core processor, with 8GB RAM, 1 TB HDD, and full HD Nvidia MX130 2G8 specification notebook. If there is anyone in here that can share the minimum requirements of the notebook, it will help me a lot to choose which one to buy. Thank you in advance. Yours faithfully, Mustafa M. Amin Consultant Psychiatrist in Biological Psychiatry Department of Psychiatry Faculty of Medicine Universitas Sumatera Utara

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Errors in WM surface persistent after manual edits to wm.mgz
by Rachel Hoel 29 Dec '18

29 Dec '18

External Email - Use Caution Dear Freesurfer Developers, Our study is implementing the longitudinal processing pipeline in FS 6.0. When attempting to make manual white matter edits to our subjects, the edits save but do not appear to impact the white matter surface. We are using the voxel-edit tool in freeview and recon-editing is selected, and the edits are made on the wm.mgz volume. Below are the commands we use to make and submit the edits... Command to open and edit WM: freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red Command to submit edits: recon-all -autorecon2-wm -autorecon3 -subjid Thank you in advance, Rachel Hoel Research Assistant Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison

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temporal lobe errors in rh.white and lh.white surfaces but not in rh.orig and lh.orig surfaces
by Neva M Corrigan 28 Dec '18

28 Dec '18

External Email - Use Caution Hi, I am using recon-all to generate pial and white matter surfaces for MPRAGE data but am having trouble in the temporal lobes for all of my subjects. The pial surfaces look very good, but the white matter surfaces are poor. Notably, the wm.mgz volume and the lh.orig and rh.orig surfaces seem to correctly include all of the white matter in the temporal lobe. However, the rh.white and lh.white surfaces miss a substantial portion of the white matter. On the ReconAllDevTable I see that the ?.orig surfaces are generated before the ?.white surfaces. Can you suggest how I might be able to fix the ?.white surfaces? In case it is relevant, I had to create an xopts.txt file with the following options in order to obtain correct skull-stripping and pial surfaces for this data: mri_normalize -mprage -b 2 -n 5 I am using freesurfer development version with a date of 05-03-2018. I have attached an image of the ?.orig and the ?.white surfaces superimposed on the wm.mgz and brainmask.mgz volumes. Thank you, Neva

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How to visualise DTI
by Renew Andrade 27 Dec '18

27 Dec '18

External Email - Use Caution Dear community! I would like to know how can I use Freeview or any tool of FreeSurfer to visualise preprocessed DTI files from a database. They are in a standard output like it appears in Tracula output page of FreeSurfer wiki. It shouldn’t be a problem to use these files in FreeSurfer. Everything (details of output and preprocessing stages) is explained in this website. https://www.nitrc.org/plugins/mwiki/index.php/neurobureau:INDIpreproc <https://www.nitrc.org/plugins/mwiki/index.php/neurobureau:INDIpreproc> Thanks for your help!

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mpr2mni305 failed, during recon-all
by Shachar Gal 24 Dec '18

24 Dec '18

External Email - Use Caution hello, I'm running the hcp's FreeSurfer pipeline, and for some reason, after working successfully several times, on different subjects, im getting this error: *** /Users/georgieboy/Research/Piano/test/222/222/mri \n mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz \n \n talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm \n ERROR: mpr2mni305 failed, see transforms/talairach_avi.log Darwin medical613-6.tau.ac.il 18.2.0 Darwin Kernel Version 18.2.0: Fri Oct 5 19:41:49 PDT 2018; root:xnu-4903.221.2~2/RELEASE_X86_64 x86_64 recon-all -s 222 exited with ERRORS at Sun Dec 23 15:50:23 IST 2018 *** the information in the talairach_avi.log is as follows: *** dyld: Symbol not found: ___keymgr_global Referenced from: /Applications/freesurfer/bin/gauss_4dfp Expected in: /usr/lib/libSystem.B.dylib in /Applications/freesurfer/bin/gauss_4dfp Abort ERROR: 'gauss_4dfp talsrcimg 1.1' failed! status=134 ERROR: mpr2mni305 execution aborted *** to be clear, this - /usr/lib/libSystem.B.dylib exists exactly where is was expected... the input image, orig.mgz, looks fine and is in 1 mm res... so im having trouble getting to the bottom of the error. thanks in advance, Shachar

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