Freesurfer

freesurfer@nmr.mgh.harvard.edu

19 participants
30088 discussions

Re: [Freesurfer] can´t open an image in Freeview
by fsbuild 22 Oct '19

22 Oct '19

External Email - Use Caution Hello Adam, Please check if you have a “freeview.bin” program. $ which freeview.bin If you get a path back with freeview.bin in it, e.g. something like/usr/local/freesurfer/bin/freeview.bin - then try the ldd command on freeview.bin, $ ldd `which freeview.bin` | grep not - then see if it lists that something is not found. - R. On Oct 19, 2019, at 03:27, Adam Rytina <adam.rytina(a)outlook.cz> wrote:        External Email - Use Caution        Hello,I run the command "$ ldd `which freeview` | grep not" and the result is "not a dynamic executable". Do you know where the problem is?What I read there could be the problem regarding 32bit or 64bit system I´m working on. I am running on Windows 10 64bit, 64 bit CPU, 64bit Ubuntu 16.04. I downloaded the 6.0.0. Freesurfer version from the official page:https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstallPlease, could you help me?Thanks a lotAdamOd: fsbuild <fsbuild@contbay.com>Odesláno: pátek 18. října 2019 22:05Komu: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>Kopie: adam.rytina@outlook.cz <adam.rytina@outlook.cz>Předmět: Re: [Freesurfer] can´t open an image in Freeview Hello Adam,See if you can run the following command, and if it reports anything is not found (you can cut and paste the command)- R.$ ldd `which freeview` | grep notAdam Rytina October 18, 2019 at 14:31        External Email - Use Caution        Hello all,I´m new to Freesurfer and I´m struggling with loading an image in FreeView. I am running the Freesurfer 6.0.0. on Ubuntu 16.04. Virtual Machine. While opening FreeView (typing "freeview" in the shell) just some empty grey windows will pop out (please see attached the screenshot). Besides this, everything is OK, I successfully tested Freesurfer installation. I haven´t found any simmilar issue on the Internet. Thus, please, could you help me to address this issue?Thanks a lotAdamBez virů. www.avast.com_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

2 1

segmentation tablet
by Lilla Zollei 22 Oct '19

22 Oct '19

Hi All, We are looking into replacing our old Wacom segmentation tablet and the two options that I have found so far are the * Wacom Cintiq Pro 32 and * Microsoft Surface Studio 2 Neither of these are linux compatible, which has created some issues in the past. Are there any groups out there who have any experience with the above (esp related to performance with FreeView) and / or any other interactive display solutions? Best, Lilla

1 0

trac-all error
by nayan wadhwani 22 Oct '19

22 Oct '19

External Email - Use Caution Hello Freesurfer, After running recon all script which completed successfully, I ran trac-all command which exited with error and tried running it with dicom files. dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib Abort ERROR: input file must be in NIfTI format Darwin EPILEPSY 16.7.0 Darwin Kernel Version 16.7.0: Mon Nov 13 21:56:25 PST 2017; root:xnu-3789.72.11~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Oct 18 22:13:02 PDT 2019 And please help me the correct config the one I created, I am attaching it below to try it with .nii files Thanks and Regards Nayan Wadhwani

2 6

tracula FA question - 2 cohorts/2 scanners
by Krieger, Donald N. 21 Oct '19

21 Oct '19

External Email - Use Caution I have tracula runs on two cohorts whose imaging was obtained on different scanners with slightly different beta's and other parameters. Would the differences in the scanners and scanning parameters be expected to produce large cohort-wide differences in the FA's? Can you point to a reference? Thanks - Don

2 2

Tracula
by Juan Rivas 21 Oct '19

21 Oct '19

External Email - Use Caution Hi, I am trying to run tracula, but I have this error: [shiraz:sub-esq-01-en] (nmr-stable53-env) trac-all -prep -c dmrirc-sub-esq-01-en INFO: SUBJECTS_DIR is /autofs/cluster/neuromod/rivas/imagenes/processing INFO: Diffusion root is /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/stable5_3_0 INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos7_x86_64-stable-v6-20161229-80ac5eb Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/freesurfer/stable5_3_0 Previous: /usr/local/freesurfer/stable6 trac-preproc -c /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/scripts/dmrirc.local -log /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/scripts/trac-all.log -cmd /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/stable5_3_0/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Oct 18 09:29:48 EDT 2019 mri_convert /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/esq-01-en_dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz mri_convert /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/esq-01-en_dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/esq-01-en_dwi.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.978979, -0.0979427, -0.178907) j_ras = (-0.0632554, 0.979704, -0.190207) k_ras = (-0.193905, 0.174892, 0.965305) writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz... cp /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/38567200_bvecs /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.mghdti.bvecs cp /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/38567200_bvals /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.mghdti.bvals flip4fsl /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -10.3297 fslswapdim /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.nii.gz x y z /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.nii.gz fslorient -forceradiological /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.nii.gz INFO: found /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.mghdti.bvals, converting to FSL format INFO: found /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig.mghdti.bvecs, converting to FSL format mv -f /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.mghdti.bvecs /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs mv -f /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.mghdti.bvals /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvals eddy_correct /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_orig_flip.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz 0 processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0000 processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0001 processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0002 processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0003 processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0004 processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0005 processing 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/autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0060 processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0061 processing /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_tmp0062 mv -f /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs.norot xfmrot /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.ecclog /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs.norot /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs ln -sf /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/data.nii.gz mri_convert --frame 0 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame0.nii.gz mri_convert --frame 0 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame0.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.978979, -0.0979427, -0.178907) j_ras = (-0.0632554, 0.979704, -0.190207) k_ras = (-0.193905, 0.174892, 0.965305) keeping frame 0 writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame0.nii.gz... mri_convert --frame 1 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame1.nii.gz mri_convert --frame 1 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame1.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.978979, -0.0979427, -0.178907) j_ras = (-0.0632554, 0.979704, -0.190207) k_ras = (-0.193905, 0.174892, 0.965305) keeping frame 1 writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame1.nii.gz... mri_convert --frame 2 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame2.nii.gz mri_convert --frame 2 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame2.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.978979, -0.0979427, -0.178907) j_ras = (-0.0632554, 0.979704, -0.190207) k_ras = (-0.193905, 0.174892, 0.965305) keeping frame 2 writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame2.nii.gz... mri_convert --frame 3 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame3.nii.gz mri_convert --frame 3 /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame3.nii.gz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.978979, -0.0979427, -0.178907) j_ras = (-0.0632554, 0.979704, -0.190207) k_ras = (-0.193905, 0.174892, 0.965305) keeping frame 3 writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame3.nii.gz... mri_concat --i /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame0.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame1.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame2.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi_frame3.nii.gz --mean --o /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb.nii.gz ninputs = 4 Checking inputs nframestot = 4 Allocing output Done allocing nframes = 4 Computing mean across frames Writing to /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb.nii.gz bet /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb_brain.nii.gz -m -f 0.5 mv -f /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb_brain_mask.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff #------------------------------------- #@# Inter-subject registration Fri Oct 18 09:57:04 EDT 2019 flirt -in /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb_brain.nii.gz -ref /usr/pubsw/packages/fsl/5.0.0/data/standard/MNI152_T1_1mm_brain.nii.gz -out /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/lowb_brain_mni.nii.gz -omat /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/diff2mni.mat -cost corratio convert_xfm -omat /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/mni2diff.mat -inverse /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/diff2mni.mat #------------------------------------- #@# Masks Fri Oct 18 09:57:39 EDT 2019 ln -sf /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff/lowb_brain_mask.nii.gz /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/nodif_brain_mask.nii.gz #------------------------------------- #@# Tensor fit Fri Oct 18 09:57:39 EDT 2019 dtifit -k /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dwi.nii.gz -m /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff/lowb_brain_mask.nii.gz -r /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvecs -b /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/bvals -o /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dtifit 0 130 0 130 0 44 0 slices processed 1 slices processed 2 slices processed 3 slices processed 4 slices processed 5 slices processed 6 slices processed 7 slices processed 8 slices processed 9 slices processed 10 slices processed 11 slices processed 12 slices processed 13 slices processed 14 slices processed 15 slices processed 16 slices processed 17 slices processed 18 slices processed 19 slices processed 20 slices processed 21 slices processed 22 slices processed 23 slices processed 24 slices processed 25 slices processed 26 slices processed 27 slices processed 28 slices processed 29 slices processed 30 slices processed 31 slices processed 32 slices processed 33 slices processed 34 slices processed 35 slices processed 36 slices processed 37 slices processed 38 slices processed 39 slices processed 40 slices processed 41 slices processed 42 slices processed 43 slices processed #------------------------------------- #@# Priors Fri Oct 18 09:57:50 EDT 2019 /usr/local/freesurfer/stable5_3_0/bin/dmri_train --outdir /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-esq-01-en.4921.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dtifit_FA.nii.gz --cptdir /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff --reg /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc ERROR: fio_pushd: /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni cwd /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en cmdline /usr/local/freesurfer/stable5_3_0/bin/dmri_train --outdir /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni --out lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr --slist /tmp/subj33.sub-esq-01-en.4921.txt --trk dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz --bmask /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/dtifit_FA.nii.gz --cptdir /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff --reg /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dmri/xfms/mni2diff.bbr.mat --ncpts 6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5 --trunc sysname Linux hostname shiraz.nmr.mgh.harvard.edu machine x86_64 user ji733 Output directory: /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/mni Output directory in test subject's space: /autofs/cluster/neuromod/rivas/imagenes/processing/sub-esq-01-en/sub-esq-01-en/dlabel/diff Output base: lh.cst_AS_avg33_mni_bbr rh.cst_AS_avg33_mni_bbr lh.unc_AS_avg33_mni_bbr rh.unc_AS_avg33_mni_bbr lh.ilf_AS_avg33_mni_bbr rh.ilf_AS_avg33_mni_bbr fmajor_PP_avg33_mni_bbr fminor_PP_avg33_mni_bbr lh.atr_PP_avg33_mni_bbr rh.atr_PP_avg33_mni_bbr lh.ccg_PP_avg33_mni_bbr rh.ccg_PP_avg33_mni_bbr lh.cab_PP_avg33_mni_bbr rh.cab_PP_avg33_mni_bbr lh.slfp_PP_avg33_mni_bbr rh.slfp_PP_avg33_mni_bbr lh.slft_PP_avg33_mni_bbr rh.slft_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.sub-esq-01-en.4921.txt Location of streamline files relative to base: dlabel/mni/lh.cst_AS.bbr.trk dlabel/mni/rh.cst_AS.bbr.trk dlabel/mni/lh.unc_AS.bbr.trk dlabel/mni/rh.unc_AS.bbr.trk dlabel/mni/lh.ilf_AS.bbr.trk dlabel/mni/rh.ilf_AS.bbr.trk dlabel/mni/fmajor_PP.bbr.trk dlabel/mni/fminor_PP.bbr.trk dlabel/mni/lh.atr_PP.bbr.trk dlabel/mni/rh.atr_PP.bbr.trk dlabel/mni/lh.ccg_PP.bbr.trk dlabel/mni/rh.ccg_PP.bbr.trk dlabel/mni/lh.cab_PP.bbr.trk dlabel/mni/rh.cab_PP.bbr.trk dlabel/mni/lh.slfp_PP.bbr.trk dlabel/mni/rh.slfp_PP.bbr.trk dlabel/mni/lh.slft_PP.bbr.trk dlabel/mni/rh.slft_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/lh.cst_AS_roi1.bbr.nii.gz dlabel/mni/rh.cst_AS_roi1.bbr.nii.gz dlabel/mni/lh.unc_AS_roi1.bbr.nii.gz dlabel/mni/rh.unc_AS_roi1.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fminor_PP_roi1.bbr.nii.gz dlabel/mni/lh.atr_PP_roi1.bbr.nii.gz dlabel/mni/rh.atr_PP_roi1.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi1.bbr.nii.gz dlabel/mni/lh.cab_PP_roi1.bbr.nii.gz dlabel/mni/rh.cab_PP_roi1.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi1.bbr.nii.gz dlabel/mni/lh.slft_PP_roi1.bbr.nii.gz dlabel/mni/rh.slft_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/lh.cst_AS_roi2.bbr.nii.gz dlabel/mni/rh.cst_AS_roi2.bbr.nii.gz dlabel/mni/lh.unc_AS_roi2.bbr.nii.gz dlabel/mni/rh.unc_AS_roi2.bbr.nii.gz dlabel/mni/lh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/rh.ilf_AS_roi2.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz dlabel/mni/fminor_PP_roi2.bbr.nii.gz dlabel/mni/lh.atr_PP_roi2.bbr.nii.gz dlabel/mni/rh.atr_PP_roi2.bbr.nii.gz dlabel/mni/lh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/rh.ccg_PP_roi2.bbr.nii.gz dlabel/mni/lh.cab_PP_roi2.bbr.nii.gz dlabel/mni/rh.cab_PP_roi2.bbr.nii.gz dlabel/mni/lh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/rh.slfp_PP_roi2.bbr.nii.gz dlabel/mni/lh.slft_PP_roi2.bbr.nii.gz dlabel/mni/rh.slft_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux shiraz.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 Fri Oct 18 09:57:50 EDT 2019 Ihave dlabel/mni folder. Could you please gimme some light about it? Thanks, JC

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Re: [Freesurfer] [EXTERNAL] Freesurfer Digest, Vol 188, Issue 32
by Xie, Hong 21 Oct '19

21 Oct '19

External Email - Use Caution Thank you -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Monday, October 21, 2019 10:33 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [EXTERNAL] Freesurfer Digest, Vol 188, Issue 32 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: FreeSurfer transforms (Bruce Fischl) 2. Re: Learning dti processing tutorial (Yendiki, Anastasia) 3. Re: can?t open an image in Freeview (fsbuild) 4. Re: aseg.stats format FreeSurfer 5 versus 6 (Tim Sch?fer) 5. Re: FSGD file formatting for Xhemi (Jose Graterol) 6. Re: FreeSurfer transforms (Vinny K) 7. tracula FA question - 2 cohorts/2 scanners (Krieger, Donald N.) 8. Incorrect/Negative Hippocampal subfields volumes (Jayachandra Raghava) 9. subcortical volume-based pet analysis (miracle ozzoude) 10. Re: imperfect segmentation in the occipital lobe in epilepsy patient (Diamond, Bram Ryder) ---------------------------------------------------------------------- Message: 1 Date: Sun, 20 Oct 2019 15:10:37 -0400 (EDT) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] FreeSurfer transforms To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <alpine.LRH.2.21.1910201509440.26358(a)door.nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" I see. Yes, a bunch of those are on our to-do list for segmentation but we don't have anything distributable at the moment. You are probably better off running some other nonlinear warping like ANTS or VoxelMorph to propagate the labels. cheers Bruce On Sat, 19 Oct 2019, Vinny K wrote: > > ????????External Email - Use Caution???????? > > Hi Bruce, > I'm looking at diencephalic and midbrain structures and their various > subdivisions for application to tractography.? I used the thalamic > nuclei segmentation feature in the development version of FreeSurfer > to obtain labeling of individual thalamic nuclei that is run in > addition to aseg, which has worked out great.? However, for other deep > brain structures such as the subthalamic or pontine nuclei (e.g. > pedunculopontine), to my knowledge, aseg does not parcellate these out; however, they are available MNI space.? > FreeSurfer gives an excellent registration?of labeled atlas structures > in patients with big ventricles, which I've had difficulty with using > other registration tools.? I was wondering if there was a way that I > could bring some of these labeled nuclei in MNI space into the > patient's T1 space using FreeSurfer. > > Thanks, > > Vinny?? > > On Sat, Oct 19, 2019 at 12:16 PM Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu> > wrote: > Hi Vinny > > why do you need to brain structures from MNI space? Isn't the > aseg > sufficient? Or are there structures that are not in the aseg? > > cheers > Bruce > On Sat, 19 Oct > 2019, Vinny K wrote: > > > > > ????????External Email - Use Caution???????? > > > > Hi, > > FreeSurfer does a great job in registering atlas structures to > patients with > > big ventricles.? I'd like to use the calculated FreeSurfer > transforms in > > bringing additional subcortical structures from MNI space > (either MNI305 or > > MNI2009b) into native T1 space.? Can you please advise on how > to do this? > > > > Thanks, > > > > Vinny?? > > > >_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA& > r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3Lpr > H61_ATtfgG0Pl3TN6dF9M&s=PGkBZSEWRaO864McYbzltpM8SlU0O1AJE6HhOS5N8bg&e= > > > ------------------------------ Message: 2 Date: Sun, 20 Oct 2019 19:23:06 +0000 From: "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Learning dti processing tutorial To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BL0PR04MB4833D9194632CC48243F2F488A6E0(a)BL0PR04MB4833.namprd04.prod.outlook.com> Content-Type: text/plain; charset="windows-1252" Hi, you need to run recon-all on the T1, not on the diffusion scan. This will produce an anatomical segmentation of each subject based on the T1s, which TRACULA will then use to extract anatomical priors on white matter tracts, to aid tractography. When you run trac-all to do the actual tractography, then you run it on the diffusion scan. ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Renew Andrade <andraderenew(a)yahoo.com> Sent: Friday, October 18, 2019 5:02:35 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Learning dti processing tutorial External Email - Use Caution I am using a database of NITRC repository https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nitrc.org_projects… . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don?t know if it is MPRAGE or not. Can you help me? What is the input file that you are supplying? Often this happens when the input it a multi-echo MPRAGE. If so, you can run mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to recon-all On 10/12/2019 4:48 PM, Renew Andrade wrote: > External Email - Use Caution > > Dear freesurfer experts: > I am trying to learn dti processing. For using Tracula it appears > there is a need for running "recon-all -all -i -s? on every subject > before starting to run Tracula. But there seems to be a problem. I > have a Parkinson dwi images database and every subject gives me an > error of the type ?input(s) cannot have multiple frames!?. I am a > little bit stuck on this step. Is it a problem of the file as input? > Am I putting the wrong file? Can it be done a recon-all analysis to a > dwi image? With trackvis I can obtain the results without any problem. > My doubt comes from FreeSurfer only and may be my little knowledge about it. > Thanks for your help! > Sincerely, > Andrade. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harv > ard.edu_mailman_listinfo_freesurfer&d=DwICAg&c=heEcP2AsrLOv4XP8e7I9NA& > r=pVcBZUHksoIOTN75JaLZTZEAPxBaNZr49Od8c24nskU&m=vTpUsyeuuJ15qFWBMe3Lpr > H61_ATtfgG0Pl3TN6dF9M&s=PGkBZSEWRaO864McYbzltpM8SlU0O1AJE6HhOS5N8bg&e= _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…

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Incorrect/Negative Hippocampal subfields volumes
by Jayachandra Raghava 21 Oct '19

21 Oct '19

External Email - Use Caution Hello Freesurfer experts & Eugenio, I have been trying to extract the volumes of hippocampal subfields using the longitudinal pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields) on macOS Mojave using freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c. For some reason, both the lh.hippoSfVolumes-T1.long.v10.txt and rh.hippoSfVolumes-T1.long.v10.txt text files show negative volumes as shown below. Hippocampal_tail -445.418232 subiculum -339.909193 CA1 -559.134087 hippocampal-fissure -165.590803 presubiculum -263.670386 parasubiculum -55.654556 molecular_layer_HP -541.803219 GC-ML-DG -293.794963 CA3 -222.042205 CA4 -266.645751 fimbria -66.106600 HATA -53.397592 Whole_hippocampus -3107.576783 I have also tried to extract the hippocampal subfield volumes from the longitudinally processed standard MNI T1 brain template (MNI152_T1_1mm_brain.nii.gz). And i still encounter the same problem with negative volumes. I could not find the suggested solution for this problem in the freesurfer mailing list. Could you please guide us on this issue? Thank you for your time and support. Best wishes Jay

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Re: [Freesurfer] FreeSurfer transforms
by Vinny K 21 Oct '19

21 Oct '19

External Email - Use Caution Hi, FreeSurfer does a great job in registering atlas structures to patients with big ventricles. I'd like to use the calculated FreeSurfer transforms in bringing additional subcortical structures from MNI space (either MNI305 or MNI2009b) into native T1 space. Can you please advise on how to do this? Thanks, Vinny

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aseg.stats format FreeSurfer 5 versus 6
by Tim Schäfer 21 Oct '19

21 Oct '19

External Email - Use Caution Dear fs experts, I'm parsing aseg.stats files for subjects to extract global brain measures and noticed that at least 2 names changed from FreeSurfer 5.1 versus FreeSurfer 6. It seems that: * "EstimatedTotalIntraCranialVol" is in v6, but "IntraCranialVol" is in v5 * "Total cerebral white matter volume" is in v6, but "Total cortical white matter volume" is in v5 Have these just been renamed, or do they carry different information? Did I overlook anything else that changed? -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

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Re: [Freesurfer] Learning dti processing tutorial
by Renew Andrade 20 Oct '19

20 Oct '19

External Email - Use Caution I am using a database of NITRC repository https://www.nitrc.org/projects/parktdi/ <https://www.nitrc.org/projects/parktdi/> . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don’t know if it is MPRAGE or not. Can you help me? What is the input file that you are supplying? Often this happens when the input it a multi-echo MPRAGE. If so, you can run mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to recon-all On 10/12/2019 4:48 PM, Renew Andrade wrote: > External Email - Use Caution > > Dear freesurfer experts: > I am trying to learn dti processing. For using Tracula it appears there is a > need for running "recon-all -all -i -s” on every subject before starting to > run Tracula. But there seems to be a problem. I have a Parkinson dwi images > database and every subject gives me an error of the type “input(s) cannot > have multiple frames!”. I am a little bit stuck on this step. Is it a problem > of the file as input? Am I putting the wrong file? Can it be done a recon-all > analysis to a dwi image? With trackvis I can obtain the results without any > problem. My doubt comes from FreeSurfer only and may be my little knowledge > about it. > Thanks for your help! > Sincerely, > Andrade. > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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