Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30065 discussions

Re: [Freesurfer] Need Urgent Help!! Regarding FreeSurfer Installation
by Tabassum, Ruchira 07 Aug '17

07 Aug '17

Can anyone provide me the link of freesurfer version 5.3 vdi file? I was trying to install it in windows 10 using virtual box, but its not working. Thanks Ruchira From: Tabassum, Ruchira Sent: Saturday, August 5, 2017 1:22 PM To: 'freesurfer(a)nmr.mgh.harvard.edu' <freesurfer(a)nmr.mgh.harvard.edu> Subject: Need Urgent Help!! Regarding FreeSurfer Installation Hi, I need Freesurfer for my windows OS. Is there any windows version of FreeSurfer? Please let me know ASAP. Kind Regards Ruchira Tabassum

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tracula problem
by Lin, Yizhi 07 Aug '17

07 Aug '17

I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Sun Aug 6 23:37:59 EDT 2017 I am sure that I have the aparc+aseg file in the right directory but it showed that the files are missing..... I would be really appreciated if anyone could please help!!! Thanks so much!!! Sincerely, Ariel

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TRACULA ERROR!!
by Lin, Yizhi 07 Aug '17

07 Aug '17

Dear fellow researchers, I am running tracula pre-processing step, and the computer showed an error message: Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux Brain 4.2.0-27-generic #32~14.04.1-Ubuntu SMP Fri Jan 22 15:32:26 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Sun Aug 6 23:37:59 EDT 2017 I am sure that I have the aparc+aseg file in the right directory but it showed that the files are missing..... I would be really appreciated if anyone could please help!!! Thanks so much!!! PS: I attached trac-all.log as an attachment. Thanks Sincerely, Ariel

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Thalamus ROI
by saraizad＠alumni.ubc.ca 07 Aug '17

07 Aug '17

Hi Freesurfer team, Is it possible to extract Thalamus as an ROI from aseg.mgz to be used for tractography in FSL. If so, what command I have to use to extract it. Can I use the LUT table to extract thalamus? Thanks, Sara

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pineal gland
by Rotem Saar 07 Aug '17

07 Aug '17

Dear Bruce and Doug, Thank u for your replay saying that it is possible to manually draw the pineal gland using freeview and extract stats for it. Can u please refer me to a link on wiki that explain how to do it? I'm not familiar with this procedure and although Doug explain it in brief I feel I need to follow some manual...is there something on the net? If not - can u please specify the steps I need to go through? Also, I have a full recon-all for the subjects I want to extract the volume of the pineal gland (using freesurfer version 3 something...). If I want to extract the volume of a specific ROI today using and advance freesurfer version (5+) - Do I need to run recon-all again with the newer version? Many thanks ! Rotem Saar-Ashkenazy Department of Brain and Cognitive Science Ben Gurion University of the Negev, Beer-Sheva, 84105 School of Social Work Ashkelon Academic College, Ashkelon, 78211 Israel

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Updating FreeSurfer v5.1 statistics to FreeSurfer v5.3
by Hatton, Sean 07 Aug '17

07 Aug '17

Hello FreeSurfer experts, I have many FS5.1 edited-subjects that I want to use in an application that only takes FS5.3 formatted statistics. I ran 20 subjects in FS51 and FS53. I took the FS51 subjects and reran recon-all -segstats (in FS53) and it updated aseg.stats closer to the values for FS53 native. I reran recon-all -parcstats but that didn't change the parcellation statistics. Correlations between FS51 updated and FS53 were ~r=0.91. It this a fair approach to take? Is there a fundamental difference between FS51 and FS53 that requires that I rerun/edit everything? Regards, Sean Hatton, PhD Postdoctoral Scholar, Department of Psychiatry UCSD

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postdoc ad
by Lilla Zollei 07 Aug '17

07 Aug '17

Please, see attached or below for details. Lilla >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Postdoctoral Research Fellow Position in Infant Brain MRI analysis at the A.A. Martinos Center, MGH and Harvard Medical School under Dr. Lilla Zöllei A postdoctoral fellow is recruited for an NIH funded project for developing Freesurfer-compatible brain image analysis tools for children. Code development will focus on pair- and group-wise registration tools, segmentation methods and surface-based image analysis algorithms. The successful applicant should have a doctoral degree in a field related to medical imaging (e.g., computer science, electrical engineering, biomedical engineering, applied mathematics, computational neuroscience). She/he is expected to have a strong research background in method development and brain image analysis and should be able to work independently. Strong programming skills (for example, C/C++, MATLAB, and/or Python) are a must and prior experience with brain image-analysis packages (such as SPM, FSL, FreeSurfer, AFNI) is desirable. In addition, the candidate must also possess excellent English verbal and written communication skills. This position will be jointly hosted by the Laboratory of Computational Neuroimaging, MGH and the Department of Psychology, Harvard University, thus the position offers great opportunities to collaborate with a large group of scientists from diverse research disciplines. Approximate start date is fall 2017. For consideration please send a statement of interest, a CV and a list of three potential references via email to Lilla Zöllei, PhD (lzollei(a)nmr.mgh.harvard.edu) The search will continue until the position is filled.

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mri_glmfit-sim output
by Van Der Deijl, Rosanne 07 Aug '17

07 Aug '17

Dear Freesurfer team, In the mri_glmfit-sim summary output file, I get a number of output variables, and I'm not sure what some of them are. Could you explain the ones in bold to me? # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPH NVtxs WghtVtx Annot 1 2.015 134872 355.89 -36.3 -9.7 -1.4 0.96620 0.96390 0.96850 841 1298.68 insula 2 1.652 71259 154.25 -49.4 -52.7 39.2 1.00000 -0.00010 1.00000 363 526.18 supramarginal 3 -1.521 91550 39.92 -37.1 -26.5 -23.3 1.00000 -0.00010 1.00000 90 -125.33 fusiform 4 1.322 139141 0.76 -36.4 3.5 -10.7 1.00000 -0.00010 1.00000 2 2.62 insula 5 1.312 73658 0.47 -36.0 -4.4 9.6 1.00000 -0.00010 1.00000 1 1.31 insula 6 1.387 133422 0.44 -5.1 -17.2 51.7 1.00000 -0.00010 1.00000 1 1.39 paracentral I know CWP stands for Cluster-wise P-value. But what is the low and the high number, a confidence interval? And isn't it odd that my p-values are (almost) 1? Thank you in advance. Kind regards, Rose

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susceptibility-induced distortions
by John Anderson 07 Aug '17

07 Aug '17

Dear Freesurfer experts, I want to inquire if there are any tools or any methods to improve T1 images which has "susceptibility-induced distortions" - attached an example. I need to fix these distortions outside the brain. In the mouth area and I am wondering what is the best approach to deal with it and fix it. I highly appreciate any help John

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Sampling vertex-wise data across various distances from the core of a mask to a somewhere else on fsaverage
by Elijah Mak 07 Aug '17

07 Aug '17

Hi Doug and Freesurfer Experts, I am trying to see whether cortical thinning gets progressively less severe as we move further away from a seed/voxel (e.g. precuneus). Is it possible to perform correlations between the (a) distance between a given vertex to specific point on fsaverage, and the (b) measurement (i.e. thickness) of the vertex? Say I have a binary mask of the precuneus seed, as well as a second binary mask that surrounds it. How may I go about getting the thickness values at various distances, starting from the central core of the precuneus seed to the outer boundary of the second mask? I was thinking of something analogous to the proj-frac function in mri_vol2surf where we could sample PET/fMRI data at different values along the cortical ribbon. Apologies if that was rather confusing. If you like, I could make a drawing of what I am trying to do. Thanks for your time. Best Wishes, Elijah

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