Freesurfer

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30084 discussions

eTIV vs. ICV
by Alexopoulos, Dimitrios 20 Apr '20

20 Apr '20

External Email - Use Caution The eTIV from FS 6.0 has been used by many as a normalization measure for regional volumetric analyses. I know it is not a true voxel count but does it conceptually include extra-axial CSF or is it more a total tissue volume? Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

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Re: [Freesurfer] [External] Freesurfer Digest, Vol 194, Issue 24
by Soichi Hayashi 20 Apr '20

20 Apr '20

External Email - Use Caution Douglas, I've uploaded my t1. It should be named "soichi-cw256.nii.gz". I am running the freesurfer with -debug option set now. I will reply back once I get the log. Thank you! Soichi On Fri, Apr 17, 2020 at 12:38 PM freesurfer-request(a)nmr.mgh.harvard.edu < freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > This message was sent from a non-IU address. Please exercise caution when > clicking links or opening attachments from external sources. > ------- > > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > 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: cw256 option not working? (Douglas N. Greve) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 17 Apr 2020 12:37:10 -0400 > From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> > Subject: Re: [Freesurfer] cw256 option not working? > To: <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: <92a8fb3b-7a8c-d31f-05c8-97983b590217(a)mgh.harvard.edu> > Content-Type: text/plain; charset="utf-8" > > Can you run it with -debug as the first option and send me the (copious) > terminal output? Even better if you can send me the data so I can try it > out in the soon-to-be-released version 7. Instructions below > > From the linux command line, > Create the file you want to upload, eg, > cd $SUBJECTS_DIR > tar cvfz subject.tar.gz ./subject > Now log? into our anonymous FTP site: > ftp surfer.nmr.mgh.harvard.edu > It will ask you for a user name: use "anonymous" (no quotes) > It will ask you for a password: use "anonymous" (no quotes) > cd transfer/incoming > binary > put subject.tar.gz > Send an email that the file has been and the name of the file. > > > On 4/17/2020 12:29 PM, Soichi Hayashi wrote: > > > > ????????External Email - Use Caution > > > > Hello. > > > > I am trying to run recon-all on HCP7T data and seeing this error message. > > > > **************************************** > > ERROR! FOV=268.800 > 256 > > Include the flag -cw256 with recon-all! > > Inspect orig.mgz to ensure the head is fully visible. > > **************************************** > > > > I've looked at orig.mgz, and it looks fine to me (screenshot attached). > > > > Anyway, I've added the -cw256 option to the command line. > > > > $ recon-all -i > > ../5e977c0dfe00f4e4b4976207/5a052586eec2b300611abffc/t1.nii.gz > > -subject output -all -parallel -openmp 8 -hippocampal-subfields-T1 > > -hires -cw256 > > > > However, I am still seeing the same error message saying that I should > > add the flag -cw256. Am I setting this option incorrectly? I am using > > freesurfer version 6.0.0. > > > > Thank you! > > Soichi Hayashi > > Screenshot from 2020-04-17 12-28-01.png > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Misalignment following bbregister
by Mason Wells 20 Apr '20

20 Apr '20

External Email - Use Caution Hi again experts, Sorry for several posts on this topic. Of the three brains I have analysed using bbregister, one of them is very misaligned. However, the FSL alignment looks fine. I ran FAST segmentation to get the white matter (pv_2) and overlaid this onto the example_func2highres.nii (see left side of attached image). However, when I view the results of bbregister (for which I used the command bbregister --s S3 --feat /Data/Feat2/S3/scans/Preprocessed_functionals/6_CMRRMB_run1_.feat/) using tkregisterfv and anat2exf.register.dat, the output is misaligned (see right of attached image). Is there a way to use the successful FSL transformation in Freesurfer, or is there any advice for correcting this misalignment? Best wishes, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk Tel: 02920 879628 Web: Cardiff University webpage <https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk Ffôn: 02920 879628

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Bad CPU type in executable
by Batra, Vinita R. 20 Apr '20

20 Apr '20

External Email - Use Caution Hello Freesurfer experts, I am currently running into an issue that I can’t seem to resolve. Is this due to incompatibilities with Mac OS Catalina ? I have the 6.0 version of Freesurfer. Would it work better with the 7.0 beta version of Freesurfer ? Please find below the output when the error occurs. The default interactive shell is now zsh. To update your account to use zsh, please run `chsh -s /bin/zsh`. For more details, please visit https://support.apple.com/kb/HT208050. Vinitas-MacBook-Pro:~ vinita$ export FREESURFER_HOME=/Applications/freesurfer Vinitas-MacBook-Pro:~ vinita$ Vinitas-MacBook-Pro:~ vinita$ export SUBJECTS_DIR=/Users/vinita/Documents/FreeSurferDirs/subjects Vinitas-MacBook-Pro:~ vinita$ Vinitas-MacBook-Pro:~ vinita$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-fsl-matlab-Darwin-OSX-stable-pub-v6.0.0-tutorial-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/vinita/Documents/FreeSurferDirs/subjects MNI_DIR /Applications/freesurfer/mni Vinitas-MacBook-Pro:~ vinita$ Vinitas-MacBook-Pro:~ vinita$ export FSL_DIR=$FREESURFER_HOME/fsl_507 Vinitas-MacBook-Pro:~ vinita$ export FSLDIR=$FSL_DIR Vinitas-MacBook-Pro:~ vinita$ cd Desktop/ Vinitas-MacBook-Pro:Desktop vinita$ trac-all -prep -c Test01.txt domainname: Command not found. export: Command not found. Too many )'s. INFO: SUBJECTS_DIR is /Users/vinita/Documents/FreeSurferDirs/subjects INFO: Diffusion root is /Users/vinita/Documents/FreeSurferDirs/subjects Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/scripts/dmrirc.local -log /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/scripts/trac-all.log -cmd /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Fri Apr 17 15:07:43 CDT 2020 mri_convert --bvec-voxel /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm... Getting Series No INFO: Found 105 files in /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI INFO: Scanning for Series Number 5 Scanning Directory INFO: found 102 files in series INFO: loading series header info. RunNo = 4 WARNING: Run 1 appears to be truncated Files Found: 102, Files Expected (lRep+1): 1 FileName /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm Identification NumarisVer syngo MR E11 ScannerModel Skyra PatientName NELSON^JAMES Date and time StudyDate 20180331 StudyTime 113843 SeriesTime 115833.384000 AcqTime 115659.267500 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_DTI PENRAD PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 4300 PhEncFOV 230 ReadoutFOV 230 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 102 SliceArraylSize 32 IsMosaic 1 ImgPos 658.2784 704.6226 66.6609 VolRes 1.7969 1.7969 4.0000 VolDim 128 128 32 Vc -0.9994 -0.0347 -0.0095 Vr 0.0349 -0.9991 -0.0241 Vs -0.0087 -0.0244 0.9997 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: sorting. INFO: (128 128 32), nframes = 102, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Could not parse NUMARIS version string syngo MR E11 found in dicom tag 18,1020 (len = 3 != 6) Repetition Time = 4300, TR = 4300 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 1.00000 0.00000 0.00000 0.00000; 0.00000 1.00000 0.00000 0.00000; 0.00000 0.00000 1.00000 0.00000; 0.00000 0.00000 0.00000 1.00000; FileName /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm Identification NumarisVer syngo MR E11 ScannerModel Skyra PatientName NELSON^JAMES Date and time StudyDate 20180331 StudyTime 113843 SeriesTime 115833.384000 AcqTime 115659.267500 Acquisition parameters PulseSeq *ep_b0 Protocol ep2d_DTI PENRAD PhEncDir COL EchoNo 1 FlipAngle 90 EchoTime 95 InversionTime -1 RepetitionTime 4300 PhEncFOV 230 ReadoutFOV 230 Image information RunNo 4 SeriesNo 5 ImageNo 1 NImageRows 768 NImageCols 768 NFrames 102 SliceArraylSize 32 IsMosaic 1 ImgPos 104.7923 113.2296 -102.6341 VolRes 1.7969 1.7969 4.0000 VolDim 128 128 32 Vc -0.9994 -0.0347 -0.0095 Vr 0.0349 -0.9991 -0.0241 Vs -0.0087 -0.0244 0.9997 VolCenter -6.6751 -7.2181 -42.5229 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 1 sagrev = 0, correv =0, trarev = 1 Vs = -0.00867384 -0.0244271 0.999664 INFO: detected a Siemens slice order reversal in mosaic, so I'm going to reverse them back to their 'original' order. TR=4300.00, TE=95.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999353, -0.0346773, -0.00951849) j_ras = (0.0348982, -0.9991, -0.0241105) k_ras = (-0.00867384, -0.0244271, 0.999664) writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz... mri_probedicom --i /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI/IM-0001-0001.dcm > /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dcminfo.dat cp /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI_bvec.txt /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvecs cp /Users/vinita/Documents/FreeSurferDirs/Data/Test01/DTI_bval.txt /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvals mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs.tmp /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvecs mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals.tmp /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvals orientLAS /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 12.915 mri_convert -oni 128 -onj 128 -onk 32 -oid -0.999353 -0.0346773 -0.00951849 -ojd -0.0348982 0.9991 0.0241105 -okd -0.00867384 -0.0244271 0.999664 -oc -6.73784 -5.42282 -42.4796 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 128 -onk 32 -oid -0.999353 -0.0346773 -0.00951849 -ojd -0.0348982 0.9991 0.0241105 -okd -0.00867384 -0.0244271 0.999664 -oc -6.73784 -5.42282 -42.4796 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999353, -0.0346773, -0.00951849) -> (-0.999353, -0.0346773, -0.00951849) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz... TR=4300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999353, -0.0346773, -0.00951849) j_ras = (0.0348982, -0.9991, -0.0241105) k_ras = (-0.00867384, -0.0244271, 0.999664) Reslicing using nearest writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz... INFO: found /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvals, copying INFO: found /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.bvecs, converting to LAS mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.bvecs /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.bvals /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals eddy_correct /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig_las.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz 0 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0000 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0001 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0002 processing 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/Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0091 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0092 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0093 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0094 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0095 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0096 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0097 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0098 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0099 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0100 processing /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_tmp0101 mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs.norot xfmrot /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs.norot /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvecs ln -sf /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/data.nii.gz mri_convert --frame 0 31 62 93 94 95 96 97 98 99 100 101 /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz mri_convert.bin --frame 0 31 62 93 94 95 96 97 98 99 100 101 /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999353, -0.0346773, -0.00951849) j_ras = (-0.0348982, 0.9991, 0.0241105) k_ras = (-0.00867384, -0.0244271, 0.999664) keeping frames 0 31 62 93 94 95 96 97 98 99 100 101 writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz... mri_concat --i /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz --mean --o /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz ninputs = 1 Checking inputs nframestot = 12 Allocing output Done allocing nframes = 12 Computing mean across frames Writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz bet /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb_brain.nii.gz -m -f 0.3 mv -f /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/lowb_brain_mask.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dlabel/diff #------------------------------------- #@# Image quality assessment Fri Apr 17 15:21:51 CDT 2020 /Applications/freesurfer/bin/dmri_motion --dwi /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz --mat /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog --bval /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals --T 229.416672 --out /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_motion.txt cwd /Users/vinita/Desktop cmdline /Applications/freesurfer/bin/dmri_motion --dwi /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz --mat /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog --bval /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals --T 229.416672 --out /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_motion.txt sysname Darwin hostname Vinitas-MacBook-Pro.local machine x86_64 user vinita Output motion measure file: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_motion.txt Input transform file: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi.ecclog Input DWI file: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz Input b-value table: /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals Low-b image intensity threshold: 229.417 Nominal diffusivity: 0.001 Loading volume-to-baseline affine transformations Computing between-volume head motion measures INFO: Processed transforms for 102 volumes Loading DWI volume series from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/dwi_orig.nii.gz Loading b-value table from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/bvals Computing within-volume head motion measures Done in 2.628 sec. dmri_motion done #------------------------------------- #@# Intra-subject registration Fri Apr 17 15:21:54 CDT 2020 mri_convert /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/mri/brain.mgz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz mri_convert.bin /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/mri/brain.mgz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/mri/brain.mgz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.29459e-10, 0) j_ras = (9.31323e-10, 1.86265e-09, -1) k_ras = (7.71252e-10, 1, 0) writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz... orientLAS /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz INFO: input image orientation is LIA INFO: input image determinant is -1 mri_convert -oni 256 -onj 256 -onk 256 -oid -1 -8.29459e-10 0 -ojd 7.71252e-10 1 0 -okd -9.31323e-10 -1.86265e-09 1 -oc -6.2289 -6.71704 -17.0073 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz mri_convert.bin -oni 256 -onj 256 -onk 256 -oid -1 -8.29459e-10 0 -ojd 7.71252e-10 1 0 -okd -9.31323e-10 -1.86265e-09 1 -oc -6.2289 -6.71704 -17.0073 -rt nearest /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz... TR=1900.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, -8.29459e-10, 0) j_ras = (9.31323e-10, 1.86265e-09, -1) k_ras = (7.71252e-10, 1, 0) Reslicing using nearest writing to /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz... tkregister2 --mov /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat_orig.nii.gz --targ /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/brain_anat.nii.gz --regheader --noedit --fslregout /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/xfms/anatorig2anat.mat --reg /Users/vinita/Documents/FreeSurferDirs/subjects/Test01_TBI3/dmri/xfms/anat2anatorig.dat /Applications/freesurfer/tktools/tkregister2.bin: Bad CPU type in executable. Darwin Vinitas-MacBook-Pro.local 19.4.0 Darwin Kernel Version 19.4.0: Wed Mar 4 22:28:40 PST 2020; root:xnu-6153.101.6~15/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Fri Apr 17 15:21:57 CDT 2020 Vinitas-MacBook-Pro:Desktop vinita$ It would be great if you could help me figure out a solution. Thanks in advance, Vinita Batra

2 1

mri_anatomical_stats - multiple subjects
by s7675854＠stud.uni-frankfurt.de 20 Apr '20

20 Apr '20

External Email - Use Caution Dear Freesurfer experts, I am trying to extract values within a ROI/label that I drew myself and registered to the subjects using mri_label2label. - is there a way to use mri_anatomical_stats for multiple subjects, so that the table output contains ROI information on all subjects and not only one (similar to e.g. aparcstats2table)? - It seems like I could use this command to extract information on e.g. thickness and surface area, but could I also use it for LGI data? (And if not, is there a different option for this measure?) Thanks a lot, Doro

2 1

recon-all in 7.0.0-beta: /usr/bin/time not installed on server, failed many hours into run
by Renner, Brian 20 Apr '20

20 Apr '20

External Email - Use Caution Hello all! A cautionary tale between versions 6.0.0 and 7.0.0. I was running recon-all as I was with version 6.0.0 and found that my runs would fail on our hpc after failing to find /usr/bin/time. This would leave it in "is-running" state. I am currently awaiting the installation of the standalone /usr/bin/time on our server and will run recon-all to see if this resolves the issue. Attached is the full log, ending with the hard exit error. Best. BR -- Brian Renner, MD Research Associate, Neurology brian.renner(a)cshs.org<mailto:brian.renner@cshs.org> Cedars-Sinai 127 S. San Vicente Blvd, Suite A6600 : Los Angeles CA 90048 office 310-423-1589 : mobile 310-658-3492 : cedars-sinai.org<https://www.cedars-sinai.org/> IMPORTANT WARNING: This message is intended for the use of the person or entity to which it is addressed and may contain information that is privileged and confidential, the disclosure of which is governed by applicable law. If the reader of this message is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this information is strictly prohibited. Thank you for your cooperation.

4 5

Most effective way to compute stats/aseg.stats
by Ерохин Александр 19 Apr '20

19 Apr '20

External Email - Use Caution Hello together, Could you please suggest the most effective way (in terms of time) for computation of statistics on segmented volumes from .nii source file? So far I went though the following steps: recon-all -autorecon1 -no-isrunning -subjid test recon-all -gcareg -no-isrunning -subjid test recon-all -canorm -no-isrunning -subjid test And seem to be stuck on -careg as transforms/talairach.m3z is needed to proceed. As far as I can tell — there is no way around recon-all -careg which seems to be the most time consuming in the chain of invocations based on Step-wise Directives ( https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all) But I might be wrong and hoping for your expertise here. Many thanks, Aleksandr Erokhin.

2 2

Data on the Freesurfer surface
by Mason Wells 18 Apr '20

18 Apr '20

External Email - Use Caution Hi all, I am trying to use an analysis package that works on surface based data (SamSrf). I have ran Feat and have a filtered_func file which is of course the motion corrected/unwarped version of my EPI. However, I need some advice on how to get these data onto the Freesurfer surface. I have found this page<https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FreeSurfer>, but I wanted to double check this is the most up-to-date pipeline. On the page it suggests using the same DOF as used in Feat, I use BBR so this seems a little redundant. Has anyone on these lists got any experience of getting filtered_func onto the Freesurfer surface? Thanks in advance, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff University Brain Research Imaging Centre (CUBRIC), School of Psychology Cardiff University Cardiff CF24 4HQ UK Email: WellsMT1(a)cardiff.ac.uk<mailto:WellsMT1@cardiff.ac.uk> Tel: 02920 879628 Web: Cardiff University webpage<https://www.cardiff.ac.uk/people/research-students/view/974214-> Mason T Wells, MSc Myfyriwr PhD Yr Ysgol Optometreg a Gwyddorau’r Golwg & Canolfan Ymchwil Delweddu’r Ymennydd Prifysgol Caerdydd (CUBRIC), Yr Ysgol Seicoleg Prifysgol Caerdydd Heol Maindy Caerdydd CF24 4HQ DU E-bost: WellsMT1(a)caerdydd.ac.uk<mailto:WellsMT1@caerdydd.ac.uk> Ffôn: 02920 879628

3 11

Re: [Freesurfer] Trac-All Error
by Hua, Jessica 17 Apr '20

17 Apr '20

External Email - Use Caution Hi Dr. Yendiki, Thanks! That fixed the issue I was having. Jessica --- Jessica Hua, M.A. Cognitive and Emotional Control Lab Doctoral Candidate Clinical Psychology University of Missouri

1 0

eTIV vs. manual ICV
by Alexopoulos, Dimitrios 17 Apr '20

17 Apr '20

External Email - Use Caution I was just wondering if using the eTIV from FS 6.0 is a reliabile measure for intracanial volume normalization. Typically, manual ICV includes extra-axial CSF which I don't think is included in the eTIV method, correct? Our population is a control adoloscent cohort and we are interested in global GM and WM, and cortical aparc volumes. Sent from Outlook Mobile<https://aka.ms/blhgte> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

1 0

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