Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

brain mask without CSF ...
by stefano.silvoni＠libero.it 18 Oct '19

18 Oct '19

External Email - Use Caution Dear FreeSurfer Experts, I am running a functional analysis of subcortical structures using FS-FAST (freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c) and I would use a brain mask excluding CSF; would it be possible using some option/flag in 'preproc-sess'? or should I do it manually? maybe using a command like that? mri_binarize --i $sbjdir/mri/aparc.a2009s+aseg.mgz --match 702 703 --o $sbjdir/mri/GM-WM_mask.mgz because I saw in FreeSurferColorLUT.txt the following definitions: 702 GrayMatter-FSL-FAST 205 62 78 0 703 WhiteMatter-FSL-FAST 0 225 0 0 or is there another strategy? thanks in advance best stefano silvoni

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covariate with repeated anova
by miracle ozzoude 18 Oct '19

18 Oct '19

External Email - Use Caution Hello Experts, I would like to include covariates in the freesurfer repeated anova steps https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova. When i tried including 3 covariates, mri_glmfit complained about "martix is ill-conditioned". How do i fix it? Below is an example my fsgd file. I've also attached the matrix design in the email. GroupDescriptorFile 1 Class PsyDis1 Class PsyDis2 Variables TP1vsTP2 Age Llesion Rlesion Input Psy1_Pre.long.Psy1 PsyDis1 1 68 96 61 Input Psy1_6mos.long.Psy1 PsyDis1 -1 68 96 61 Input Psy2_Pre.long.Psy2 PsyDis2 1 39 217 140 Input Psy2_6mos.long.Psy2 PsyDis2 -1 39 217 140 contrast: 0 0 1 0 0 Best, Paul

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Re: [Freesurfer] Download link broken
by Hoopes, Andrew 18 Oct '19

18 Oct '19

Hi Tashrif, sorry, we had a network outage last night, but the link should be fixed now. best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Billah, Tashrif" <tbillah(a)bwh.harvard.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Friday, October 18, 2019 at 10:08 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Download link broken Hi FreeSurfer team, The following link appears broken since 10/17 evening. https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin… Can you look into it? Best, Tashrif ------------------------------------------------------------- Tashrif Billah, MS Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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Download link broken
by Billah, Tashrif 18 Oct '19

18 Oct '19

Hi FreeSurfer team, The following link appears broken since 10/17 evening. https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Lin… Can you look into it? Best, Tashrif ------------------------------------------------------------- Tashrif Billah, MS<https://www.linkedin.com/in/tashrif-billah/> Research Engineer Brigham and Women's Hospital Harvard Medical School tbillah(a)bwh.harvard.edu<mailto:tbillah@bwh.harvard.edu> http://pnl.bwh.harvard.edu/tashrif-billah-m-s/

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QDEC cluster output
by Lara Foland-Ross 18 Oct '19

18 Oct '19

External Email - Use Caution Hi Freesurfer experts, I’m running a simple qdec analysis to examine group differences in surface measures between a patient and control group, controlling for age and TBV. I noticed that when I run Monte Carlo Simulations (threshold=1.3, sign=abs), I get the following output in my terminal window: ~~~~~~~~~~~~ # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZ CWP CWPLow CWPHi NVtxs Annot 1 7.365 125481 2114.03 -34.4 4.1 1.6 0.01660 0.01500 0.01820 4933 insula 2 3.851 73048 1830.45 -8.4 30.1 29.4 0.03440 0.03210 0.03670 3210 superiorfrontal 3 -3.248 128137 4923.73 -8.1 -64.0 5.8 0.00010 0.00000 0.00020 7680 lingual Simulation complete. ~~~~~~~~~~~~ However, when I click on “Find clusters and go to max”, the output in my terminal window changes to be as follows: ~~~~~~~~~~~~ Generating cluster stats using min threshold of 1.3... Found 3 clusters Contrast: 'lh-Diff-Control-Klinefelter-Intercept-volume', 20fwhm, DOF: 35 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -4.0000 33 4923.73 -12.0 -67.1 34.7 7680 precuneus 2 1.7799 9 2114.03 -26.3 23.8 -6.0 4933 lateralorbitofrontal 3 1.4634 21 1830.45 -6.6 33.8 49.8 3210 superiorfrontal ~~~~~~~~~~~~ Lastly, I see that the x/y/z coordinates of the peak coordinates listed above are on the very edge of the corrected cluster. Yet, visual inspection of the peaks from uncorrected significance maps suggest that the peaks it is quite far from the “hottest” parts of the uncorrected significance maps. My questions are: 1. Why are these values different, and what values should I report? 2. Are the peaks listed above the center of gravity? Or highest p value of the cluster? Curious as to why the heatmap values are so different from the values above. Many thanks, Lara

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Re: [Freesurfer] ERROR gtmseg
by Marina Fernández 18 Oct '19

18 Oct '19

External Email - Use Caution Dear Douglas, Did you get the subjects? I hope I loaded them correctly. Best regards, Marina.

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mri_pretess: Cannot allocate memory
by Peled, Noam 17 Oct '19

17 Oct '19

Dear group, When trying to run mri_pretess, I'm getting this error: znzTAGskip: tag=809120822, failed to calloc 1802706944 bytes! Cannot allocate memory Here is the full command I'm using (in the Martinos center, using ver6 stable): mri_pretess /autofs/space/thibault_001/users/npeled/subjects/mg27/mri/aseg.mgz 54 /autofs/space/thibault_001/users/npeled/subjects/mg27/mri/norm.mgz /autofs/space/thibault_001/users/npeled/subjects/mg27/tmp/274f23/54_filled.mgz Thanks! Noam

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Tracula question
by Alan Francis 17 Oct '19

17 Oct '19

External Email - Use Caution Dear Anastasia - I tried running tracula preproc. However, it gave me an error message. Could you please shed some light on this? Thank you, Alan [airhunger:JC_DTI] (nmr-stable6-env) trac-all -prep -c dmrirc-esq-14-hc INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC INFO: Diffusion root is /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos7_x86_64/stable6 trac-preproc -c /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/dmrirc.local -log /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.log -cmd /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable6/bin/trac-preproc #------------------------------------- #@# Image corrections Tue Oct 15 10:01:10 EDT 2019 mri_convert --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/esq-14-hc_dwi.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs cp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/31916396_bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals.tmp /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals orientLAS /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -18.7806 mri_convert -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 130 -onj 130 -onk 24 -oid -0.996936 0.0343122 -0.0703008 -ojd 0.0173889 0.973389 0.228497 -okd -0.0762703 -0.226574 0.971003 -oc -0.761131 24.2246 -3.09646 -rt nearest /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.996936, 0.0343122, -0.0703008) -> (-0.996936, 0.0343122, -0.0703008) normalizing out_j_direction: (0.0173889, 0.973389, 0.228497) -> (0.0173889, 0.973389, 0.228497) normalizing out_k_direction: (-0.0762703, -0.226574, 0.971003) -> (-0.0762703, -0.226574, 0.971003) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) Reslicing using nearest writing to /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz... INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvals, copying INFO: found /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig.bvecs, converting to LAS mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.bvals /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvals eddy_correct /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_orig_las.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz 0 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0000 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0001 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0002 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0003 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0004 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0005 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0006 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0007 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0008 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0009 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0010 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0011 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0012 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0013 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0014 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0015 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0016 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0017 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0018 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0019 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0020 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0021 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0022 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0023 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0024 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0025 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0026 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0027 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0028 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0029 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0030 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0031 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0032 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0033 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0034 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0035 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0036 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0037 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0038 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0039 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0040 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0041 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0042 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0043 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0044 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0045 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0046 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0047 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0048 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0049 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0050 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0051 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0052 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0053 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0054 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0055 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0056 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0057 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0058 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0059 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0060 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0061 processing /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi_tmp0062 mv -f /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot xfmrot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.ecclog /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs.norot /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. ln -sf /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/data.nii.gz mri_convert --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz mri_convert.bin --frame 63 /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /autofs/cluster/neuromod/JC_DTI/ESQ_14_HC/ESQ_14_HC/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.996936, 0.0343122, -0.0703008) j_ras = (0.0173889, 0.973389, 0.228497) k_ras = (-0.0762703, -0.226574, 0.971003) keeping frame 63 ERROR: valid frame numbers are between 0 and 62 Linux airhunger.nmr.mgh.harvard.edu 3.10.0-957.1.3.el7.x86_64 #1 SMP Thu Nov 29 14:49:43 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux trac-preproc exited with ERRORS at Tue Oct 15 10:17:55 EDT 2019 -- *|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|* *Alan N. Francis PhDInstructor in PsychiatryHarvard Medical School* *Louis V. Gerstner III scholarMartinos Center for Biomedical Imaging* *Massachusetts General Hospital* *149, 13th street, Charlestown, MA* *alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> * *afrancis(a)mclean.harvard.edu <afrancis(a)mclean.harvard.edu>*

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FreeSurfer mal list - please remove me
by Adam Rytina 17 Oct '19

17 Oct '19

External Email - Use Caution Hello all, few days ago I subscribed to the FreeSurfer list in order to get e-mails regarding the FreeSurfer issues. I will not use FreeSurfer anymore. Hence, please, could you remove me from this list? Thanks a lot Adam

3 2

freeview: load multiple volumes with a single option
by Jang, Ikbeom 16 Oct '19

16 Oct '19

Dear FreeSurfer community: I am a beginner and tying to load multiple volumes in Freeview with a single option applied to all the volumes. For example, I would like to set grayscale window as min=0 and max=100 for all volumes. Is there a simple command line which does that efficiently? The command line below works if I provide the option for each volume: freeview -v sitename/mri/subj0401/brainmask.mgz:grayscale=0,100 \ sitename/mri/subj0402/brainmask.mgz:grayscale=0,100 \ ... \ sitename/mri/subj0425/brainmask.mgz:grayscale=0,100 However, the command line something like this does not: freeview -v sitename/mri/subj*/brainmask.mgz:grayscale=0,100 Thanks in advance, Ikbeom

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