Freesurfer February 2018

freesurfer@nmr.mgh.harvard.edu

119 participants
170 discussions

Funded PhD at Cardiff University in collaboration with UCL and University of Wisconsin-Madison on Brain Complexity and Consciousness
by Chen Song 11 Feb '18

11 Feb '18

*PhD Project: Brain Complexity and Consciousness* *Application Deadline: Feb 23, 2018* Applications are invited for a PhD studentship to work with Dr. Chen Song <https://www.braincomplexity.com/> and Prof. Derek Jones <http://psych.cf.ac.uk/contactsandpeople/jonesd27.php> at Cardiff University Brain Research Imaging Centre (CUBRIC), one of Europe’s largest brain research centres, in collaboration with Prof. Geraint Rees <https://en.wikipedia.org/wiki/Geraint_Rees> at University College London and Prof. Giulio Tononi <https://en.wikipedia.org/wiki/Giulio_Tononi> at University of Wisconsin-Madison. This PhD studentship offers an excellent opportunity for candidates interested in the broad area of brain imaging, neuroscience, and/or consciousness research, to conduct research on the following topics: - *Brain complexity* - how different brain regions differ structurally, how their structural differences underpin their functional differences, whether the empirically-observed function of a brain region is what the structure of this brain region is theoretically optimal for; - *Mapping between brain complexity and consciousness* - how different individuals differ in their brain structure, how the inter-individual differences in brain structure affect brain function, and lead to inter-individual differences in perception and cognition; - *Brain plasticity* - how learning and sleep interact to change brain structure and function, whether different mechanisms of brain plasticity may be at play during wake versus sleep, and whether the contrast between the two may hold key to our intelligence and consciousness. See some of our recent work on these topics at: Schwarzkopf et al. Nature Neuroscience 2010 <https://www.nature.com/articles/nn.2706>; Song et al. Journal of Neuroscience 2011 <http://www.jneurosci.org/content/31/26/9472.long>; Song et al. Journal of Neuroscience 2013 <http://www.jneurosci.org/content/33/48/18781.long>; Song et al. Nature Communications 2013 <https://www.nature.com/articles/ncomms3201>; Tononi et al. Neuron 2014 <http://www.cell.com/neuron/fulltext/S0896-6273(13)01186-0>; Song et al. Neuron 2015 <http://www.cell.com/neuron/fulltext/S0896-6273(14)01150-7>; Tononi et al. Nature Reviews Neuroscience 2016 <https://www.nature.com/articles/nrn.2016.44>; Song et al. Journal of Neuroscience 2017 <http://www.jneurosci.org/content/37/37/8929.long>; or a summary at: http://www.braincomplexity.com/research. The successful applicant will be able to use the *£44M cutting-edge brain imaging facilities at CUBRIC* to acquire multi-modal brain measures (structural, metabolic, electrical, chemical), and link the empirical data to theories on brain complexity and consciousness (integrated information theory), sleep and cognition (synaptic homeostasis hypothesis). As one of Europe’s largest brain research centres, CUBRIC hosts: - one of the only three Connectom MRI scanners in the world, specially designed for measuring brain microstructure and connectomics; - one 7T MRI scanner, two 3T MRI scanners, one MEG scanner, three EEG labs, five TMS labs; - six sleep study bedrooms built to clinical standard. The studentship is open to UK/EU/international students; it covers the full tuition fee (at UK/EU level) and an annual stipend of £14,553. Please contact Dr. Chen Song at SongC5(a)cardiff.ac.uk for any enquiries, or see application details at http://psych.cf.ac.uk/degre eprogrammes/postgraduate/research/docs/school_song.pdf.

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Two versions of FreeSurfer in the same computer
by Vania de Aguiar 09 Feb '18

09 Feb '18

Dear, I will be attending the workshop in April and I started taking the tutorials online to get prepared. My laptop is running an older of freesurfer (5.0.0), because I have data to add to other data analysed by a previous lab member. I am aware that I shouldn't mix versions, but for tutorials and the workshop I think it would be best to work on the newest version. Can I have both versions running in my computer, to use one for that project and the other one for current tutorials and the workshop? ?Best, Vânia de Aguiar, PhD Postdoctoral research fellow Johns Hopkins Medical Institute Department of Neurology 600 N. Wolfe street, Phipps 477 Baltimore, MD, 21287 Phone: +1 (410) 955 8210

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no white matter is labelled when using mri_aparc2aseg
by Sims, Sara A 09 Feb '18

09 Feb '18

Doug, I am sorry that I wasn’t clear before, here is all the info about it all in one place. I am trying to transfer a cortical label to label wm by using the following commands: subjects=/data/user/snolin/Scripts/Freesurfer_scripts/partial_recon; unset SUBJECTS_DIR SUBJECTS_DIR=$subjects export SUBJECTS_DIR patient=211215 #Label 8 conversion mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab --s $patient --h lh --l $subjects/$patient/label/8_LH_V1.label --a 8V1 mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab --s $patient --h rh --l $subjects/$patient/label/8_RH_V1.label --a 8V1 mri_aparc2aseg --s $patient --annot 8V1 --labelwm mri_binarize --i $subjects/$patient/mri/8V1+aseg.mgz --o $subjects/$patient/mri/8V1_bin.mgz --match 4001 3001 mri_convert $subjects/$patient/mri/8V1_bin.mgz $subjects/$patient/mri/8V1_bin.nii mri_vol2vol --mov /data/project/vislab/raw/HCP_900sub/HCP_diff_data/$patient/data.nii.gz --targ $subjects/$patient/mri/8V1_bin.nii --reg /data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/$patient/register_edit.dat --o $subjects/$patient/mri/8V1_diffROI.nii --inv --nearest This makes a 8V1+aseg.mgz file there are just no 4001 and 3001's in the file so when I binarize there is nothing there. So my question is why is it not identifying the wm next to my label? This is happening in multiple subjects on varying labels. I have attached a picture of what the error looks like. As you can see all the values in the volume are all zero (blue) and there is nothing next to the cortical label (red). I have tried changing the -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I could find but it won’t budge even though doing other labels in the same person works fine. The original cortical label is also correctly placed in the cortical ribbon. Here is the output from running the above commands: Reading ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab Number of ctab entries 2 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data/user/snolin/Scripts/Labelmaker cmdline mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab --s 211215 --h lh --l /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_LH_V1.label --a 8V1 sysname Linux hostname c0039 machine x86_64 user snolin subject 211215 hemi lh SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon ColorTable /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8lhV1.ctab AnnotName 8V1 nlables 1 LabelThresh 0 0.000000 ERROR: /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot already exists Reading ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab Number of ctab entries 2 $Id: mris_label2annot.c,v 1.20 2016/01/07 23:28:11 greve Exp $ cwd /data/user/snolin/Scripts/Labelmaker cmdline mris_label2annot --ctab /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab --s 211215 --h rh --l /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/8_RH_V1.label --a 8V1 sysname Linux hostname c0039 machine x86_64 user snolin subject 211215 hemi rh SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon ColorTable /data/user/snolin/Scripts/Labelmaker/color_tables/clut.8rhV1.ctab AnnotName 8V1 nlables 1 LabelThresh 0 0.000000 ERROR: /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot already exists SUBJECTS_DIR /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon subject 211215 outvol /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz useribbon 0 baseoffset 0 labeling wm dmaxctx 5.000000 RipUnknown 0 Reading lh white surface /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.white Reading lh pial surface /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/lh.pial Loading lh annotations from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/lh.8V1.annot Reading rh white surface /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.white Reading rh pial surface /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/surf/rh.pial Loading rh annotations from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/label/rh.8V1.annot Loading ribbon segmentation from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/ribbon.mgz Building hash of lh white Building hash of lh pial Building hash of rh white Building hash of rh pial Loading aseg from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/aseg.mgz ASeg Vox2RAS: ----------- -1.00000 0.00000 0.00000 128.00000; 0.00000 0.00000 1.00000 -128.00000; 0.00000 -1.00000 0.00000 128.00000; 0.00000 0.00000 0.00000 1.00000; ------------------------- Labeling Slice 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 nctx = 1124316 Used brute-force search on 0 voxels Fixing Parahip LH WM Found 0 clusters Fixing Parahip RH WM Found 0 clusters Writing output aseg to /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz $Id: mri_binarize.c,v 1.43 2016/06/09 20:46:21 greve Exp $ cwd /data/user/snolin/Scripts/Labelmaker cmdline mri_binarize.bin --i /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz --o /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz --match 4001 3001 sysname Linux hostname c0039 machine x86_64 user snolin input /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1+aseg.mgz frame 0 nErode3d 0 nErode2d 0 output /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz Binarizing based on matching values nMatch 2 0 4001 1 3001 binval 1 binvalnot 0 fstart = 0, fend = 0, nframes = 1 Found 0 values in range Counting number of voxels in first frame Found 0 voxels in final mask Count: 0 0.000000 16777216 0.000000 mri_binarize done mri_convert.bin /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) writing to /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii... Matrix from regfile: 1.00000 -0.00055 0.00091 -0.38465; -0.00091 0.00095 1.00000 0.38039; -0.00055 -1.00000 0.00095 -0.14575; 0.00000 0.00000 0.00000 1.00000; movvol /data/project/vislab/raw/HCP_900sub/HCP_diff_data/211215/data.nii.gz targvol /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_bin.nii outvol /data/user/snolin/Scripts/Freesurfer_scripts/partial_recon/211215/mri/8V1_diffROI.nii regfile /data/user/snolin/HCP_registration/HCP_BBR/HCP_registration_new/211215/register_edit.dat invert 1 tal 0 talres 2 regheader 0 noresample 0 interp nearest (0) precision float (3) Gdiag_no -1 Synth 0 SynthSeed 1518108582 Invert! Inverting registration Final tkRAS-to-tkRAS Matrix is: 1.00000 -0.00091 -0.00055 0.38491; -0.00055 0.00095 -1.00000 -0.14632; 0.00091 1.00000 0.00095 -0.37990; 0.00000 0.00000 0.00000 1.00000; Vox2Vox Matrix is: 1.25000 -0.00069 0.00114 36.96743; 0.00114 0.00118 -1.25000 218.81943; 0.00069 1.25000 0.00118 18.96824; 0.00000 0.00000 0.00000 1.00000; Resampling Output registration matrix is identity mri_vol2vol done Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin(a)uab.edu

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shift to account for hemodynamic response
by Ashley Cole 09 Feb '18

09 Feb '18

Dear experts, I just have switched from SPM to Freesurfer. I am wondering if in FSFAST analysis, we require to shift the regressors in time to account for the delay in hemodynamic response? Thanks

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fmri_readreg
by shahin＠nmr.mgh.harvard.edu 09 Feb '18

09 Feb '18

Dear Surfers, Previously we had a matlab function fmri_readreg.m (author: Doug Greve) that could extract the regmat from the register.dof6.dat files. But version 6 does not generate dof6.dat anymore. Rather it generates a dof6.lta that fmri_readreg can not read. I was wondering if there is an updated version of fmri_readreg.m to read lta files. If no, would you tell me how to extract regmat from this lta file. regards _____________________________________ Shahin Nasr Assistant Prof. in Radiology Harvard Medical School Martinos Imaging Center, MGH Bldg 149, 13th street, Charlestown, MA 02129

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[freesurfer] Extracting values of cortical thickness in each vertex.
by 박경일 09 Feb '18

09 Feb '18

Dear FS experts, I could get QDEC image comparing two groups. However, is there a way to get numerical values of cortical thickness in each vertex? Thank you Best, Kyung

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How to analyze fMRI in native volume space
by Tuominen, Lauri Johannes 09 Feb '18

09 Feb '18

Dear Freesurfers! I would like have my fMRI runs in the native T1 volume space and do the first level analyses there. I can only find -self flag for surface based analyses in preproc-sess. What would be there recommended way to do the analyses in the T1 volume space? This is 7T data and I’d like to use the individual segmentations as ROIs. Thank you so much! Lauri Tuominen

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Multiple regression FreeSurfer
by Martin Juneja 09 Feb '18

09 Feb '18

Hi, I am interested in correlating cortical volume measures with behavioral data X1, after regressing out the effect of age and sex. For that I ran following commands: mri_glmfit --y lh.X1.CV.15.mgh --fsgd X1.fsgd dods --C Corr-X1-cor.mtx --surf fsaverage lh --cortex --glmdir lh.X1_CV.glmdir mri_glmfit-sim --glmdir lh.X1_CV.glmdir --cache 2 abs --cwp 0.05 --2spaces where X1.fsgd is following: GroupDescriptorFile 1 Class Male Class Female Variables X1 Age Input S001 Male 127 36 .... so on and Corr-X1-cor.mtx is 0 0 0 0 1 I was wondering how can I use multiple regression approach e.g. how can I correlate CV and X1 after accounting for thickness and area or how can I correlate gyrification and X1 after accounting for CV and thickness etc. I am not sure what will be my commands for that and what will be fsgd and mtx files? Thanks for your help.

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Gray matter mask
by Hanna Vasilevskaya 09 Feb '18

09 Feb '18

Hello FS team, I am new to FS and using version 5.3 on a Mac. I have minimal programming background and this might be a very easy question, however I was not able to find a similar one in the archive. I have T1 MRI images from multiple subjects and I need to extract the brain gray matter mask (just cortical regions, without cerebellum). I will then use this mask as an ROI to extract PET activity. Would you happen to know a way for this? Thank you greatly, Anna

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mri_aparc2aseg labelwm not labelling wm
by Sims, Sara A 09 Feb '18

09 Feb '18

Freesurfers, I am trying to use a cortical label to label wm. I am using the following command line: mri_aparc2aseg --s $patient --annot 8V1 –labelwm And most of the time in most subjects this works, however sometimes the output file doesn’t label any wm with the 3000+N or 4000+N like it usually does. I have tried changing the -wmparc-dmax, -hypo-as-wm, -smooth_normals. Basically everything I could find but it won’t budge even though doing other labels in the same person works fine. Fyi: The original cortical label is also correctly place in the cortical ribbon. Any ideas? Please! Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin(a)uab.edu

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Freesurfer February 2018