Freesurfer December 2018

freesurfer@nmr.mgh.harvard.edu

109 participants
175 discussions

segmentHA_T2 newbie questions
by Freesurfer 11 Dec '18

11 Dec '18

External Email - Use Caution Hi, Trying to run the HippoAmig segmentation with T1-w and T2-w files for the first time and I have a few basic questions I could not resolve looking on the FS wiki: 1. Does the T2-w image need to be first recon-all processed like the T1-w? On the wiki the command line is: segmentHA_T2.sh bert FILE_ADDITIONAL_SCAN ANALYSIS_ID USE_T1 2. Does “bert” correspond to the directory for recon-all subject “bert” after been processed? 3. Does the FILE_ADDITIONAL_SCAN need to be a nit scan or should it point to the freesurfer directory post recon-all (this is kind of related to question #1 I realize). 4. In ANALYSIS_IS can I type just “T2”? Thanks! K

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Freeview Scrolling through slices on a Mac
by Chris Petty 11 Dec '18

11 Dec '18

External Email - Use Caution Maybe I am missing something, but how can I scroll through slices with keyboard or mouse in Freeview on a Mac? Nothing I’ve tried works thus far. Any typical key ( cmd, ctrl, shift ) with scroll just zooms. Up/down moves the image up and down … shift / option / cmd with up / down either zooms or moves up / down. I’m just trying to add control points and definitely need to scroll through slices without clicking on the image. Thanks, -Chris

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Version 6.0.0 or 6.0.1?
by Kirstie Whitaker 11 Dec '18

11 Dec '18

External Email - Use Caution Hi Freesurfer team, On the download website version 6.0.0 is linked: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall But on this list there has been discussion of version 6.0.1 which can be downloaded from https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1 What's the recommended version to use? I've been using 6.0.0 but with an updated make file following the instructions in this email: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056644.ht… Is the makefile updated in 6.0.1? Are there any other differences? I'm having a lot of difficulty getting recon-all to run reliably with 6.0.0 (some subjects are fine, others not!) and I'm wondering if that's because I'm supposed to be using 6.0.1? Thank you for your help! Kirstie -- Kirstie Whitaker, PhD Research Fellow, Alan Turing Institute Research Associate, University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* https://whitakerlab.github.io *Twitter:* @kirstie_j <https://twitter.com/kirstie_j>

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Re: [Freesurfer] Recon command with T1 and T2
by Maksimovskiy, Arkadiy 11 Dec '18

11 Dec '18

Thank you Doug. Much appreciated. -arkadiy

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Recon command with T1 and T2
by Maksimovskiy, Arkadiy 11 Dec '18

11 Dec '18

Dear Experts, I am planning to run "recon" using T1 and T2 images, and was wondering if you wouldn't mind confirming whether this is the right command with recon: recon-all -s ${subject} -i T1.nii -T2 T2.nii -all I have seen a slightly different variation in the mailing archives, but this was years ago, and I believe that mine is consistent with the Wiki. Additionally, should the -T2pial flag be included? Thank you for your help, Arkadiy -- Arkadiy L. Maksimovskiy, Ph.D. <https://www.researchgate.net/profile/Arkadiy_Maksimovskiy2> Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Command to convert subcortical values into subcortical segmentation
by Conchy PF 11 Dec '18

11 Dec '18

External Email - Use Caution Hello FS experts, I was wondering if there is a command similar to annotval2surfoverlay.m that allows converting subcortical values into aseg.annot subcortical segmentation. Thank you in advance and kind regards, Lisbeth

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Re: [Freesurfer] Increasing the Number of a non-FreeSurfer Parcellation
by Maedeh Khalilian 11 Dec '18

11 Dec '18

External Email - Use Caution Dear Bruce The parcellation I have is not on surface, it is volumetric. I wanna increase the number of its ROIs, I thought maybe I can change it into an annotation file and then use "mris_divide_parcellation". Hope it is clear enough now. Best Maedeh

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GLM multiple comparison correction
by Barletta, Valeria 11 Dec '18

11 Dec '18

Good morning! We are running a GLM with two groups (patients versus controls) and one variable (age). We are using the following option to correct for multiple comparisons: mri_glmfit-sim --glmdir ${glm_dir}/${hemi}_contrast-${contrast}_${surfname_t1} --cache 1.3 pos If we change the option "pos" with "neg" or "abs", we obtain exactly the same cluster (attached). Is this normal? What is the option "pos" staying for exactly? Thanks, Valeria

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glm analysis
by Barletta, Valeria 11 Dec '18

11 Dec '18

Dear Freesurfers, I am trying to run a GLM analysis with 3 groups (1)long disease duration MS, 2)short disease duration MS, 3)healthy controls) and 1 variable (age). According to the formula provided on freewiki: N classes (N of variables + 1), is this contrast matrix correct? 1 -1 0 0 0 0 1 0 -1 0 0 0 thank you, Valeria

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fdr correction problem
by 1013364183 11 Dec '18

11 Dec '18

External Email - Use Caution Dear Bruce， I have fdr correction for sig.mgh obtained by mri_glmfit, but the corrected graphs are all 0. Why is this, the instructions and the running results are as follows: mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh $Id: mri_fdr.c,v 1.2 2016/01/07 22:23:57 greve Exp $ cwd /usr/local/freesurfer/subjects cmdline mri_fdr --fdr .05 --i lh2.gender_age.glmdir/group2/sig.mgh lh2.gender_age.glmdir/mask.mgh 2.mgh sysname Linux hostname xiaorn machine x86_64 user xiaorn fdr 0.050000 ninputs 1 MRIfdr2vwth: np = 149953, nv = 163842 MRIfdr2vwth: vwth = 0.000003, log10(vwhth) = 5.583609 voxel-wise-threshold 5.5836093010 Writing to 2.mgh mri_fdr done yours yujunjie

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Freesurfer December 2018