Freesurfer

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30132 discussions

mris_ca_label seed
by Rosemary Nicholas 11 Jul '18

11 Jul '18

External Email - Use Caution Hello, I am running a dataset through version 6.0 of Freesurfer on Linux, extracting results for both the Desikan atlas and our own atlas. When extracting the stats for our atlas, the results were varying considerably (sometimes up to 10%) in test-retest runs. The release notes for 4.5 indicate that the default setting for mris_ca_label should use the same number as a seed, and therefore give the same results, but it doesn't. "The binaries in the recon-all stream which are subject to variability due to usage of a random number generator (mris_smooth, mris_sphere, mris_topology_fixer, mris_topo_fixer and mris_ca_label) are now seeded with the same number, with the result being that repeated runs of the recon-all stream on a subject on the same platform will always give identical results." The issue seems to be resolved by adding -seed 1234 as a flag to mris_ca_label. I would like to understand what this is actually doing though, before applying it to all my data. What is the random number generator used for? What does setting it to 1234 actually do? It isn't listed in the optional flagged arguments. Is it just deciding which vertex is labeled first? Here is how we are running it (in two independent scripts): FIRST: # autorecon1 including data conversion recon-all -i $mprage/001 -autorecon1 -subjid $s # autorecon2 with threshold adjustments recon-all -seg-wlo 60 -seg-ghi 70 -autorecon2 -subjid $s # autorecon3 recon-all -autorecon3 -subjid $s THEN: mris_ca_label $s $h sphere.reg /g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot modified to: mris_ca_label -seed 1234 $s $h sphere.reg /g5/dcn/freesurfer_testing/subjects/"$h".rantaFL.gcs rantaFL.annot Thank you, Rosemary Nicholas Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute

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/run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.
by Jasmin Alves 11 Jul '18

11 Jul '18

External Email - Use Caution Hello FreeSurfer Developers, I am trying to analyze the subfields of the hippocampus using FreeSurfer 6.0 based on the tutorial, "Segmentation of hippocampal subfields". However, several errors come up when I run: recon-all -s 102 -hippocampal-subfields-T1 #@# Hippocampal Subfields processing (T1 only) left Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. #-------------------------------------------- #@# Hippocampal Subfields processing (T1 only) right Tue Jul 10 20:20:18 PDT 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found. I have searched through the list to see if anyone else has had this issue but to no avail. Version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c OS: X V 10.9.5 Thanks! Jasmin -- Jasmin Alves Doctoral Candidate Medical Biology Graduate Program University of Southern California jalves(a)usc.edu

2 5

recon-all fatal error
by Daniel Kimmel 11 Jul '18

11 Jul '18

External Email - Use Caution Hello, I'm attempting to run basic preprocessing with reconstruction using fmriprep-docker.py and freesurfer. The fmriprep process completes when excluding freesurfer, but encounters a fatal error when including freesurfer. There error is: recon-all -s sub-18042401 exited with ERRORS at Wed Jul 11 01:39:47 UTC 2018 For more details, see the log file /out/freesurfer/sub-18042401/scripts/recon-all-rh.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> Standard error: ln: failed to create symbolic link 'rh.white.H': Operation not supported Return code: 1 180711-01:39:51,447 workflow ERROR: could not run node: fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs 180711-01:39:51,452 workflow ERROR: could not run node: fmriprep_wf.single_subject_18042401_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs 180711-01:39:54,738 cli WARNING: Errors occurred while generating reports for participants: 18042401 (2). The call to freesurfer is made by fmriprep, which is doing so within a docker container, so unfortunately I don't know the exact version of freesurfer. I'm using fmriprep version 1.0.13. I make the call to fmriprep from a CentOS Linux box: uname -a: Linux xxx.xxx.xxx.columbia.edu <http://xxx.xxx.xxx.columbia.edu/> 3.10.0-862.2.3.el7.x86_64 #1 SMP Wed May 9 18:05:47 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux I've attached: 1) the complete terminal output from fmriprep (which is reporting the output of freesurfer) 2) recon-all-status-rh.log 3) recon-all.log Thanks very much for your help! Best, Daniel

2 2

ERROR: Transform file should be eddy_correct/eddy log file or .mat file
by Renew Andrade 11 Jul '18

11 Jul '18

External Email - Use Caution Hello: I have a problem when running trac-all preprocessing. I have X11 and FSL installed. Not Matlab I don’t know if I need it I think only for fMRI. Sincerely, Andrade. Renes-MacBook-Air-2:diffusion_tutorial andraderenew$ trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial INFO: SUBJECTS_DIR is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_recons INFO: Diffusion root is /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial Actual FREESURFER_HOME /Applications/freesurfer INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20130423 Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /usr/local/freesurfer/dev trac-preproc -c /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/dmrirc.local -log /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.log -cmd /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/scripts/trac-all.cmd #------------------------------------- /Applications/freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Wed Jul 11 17:53:23 CEST 2018 mri_convert --bvec-voxel /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm... Getting Series No INFO: Found 75 files in /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig INFO: Scanning for Series Number 11 Scanning Directory INFO: found 70 files in series INFO: loading series header info. RunNo = 10 WARNING: Run 1 appears to be truncated Files Found: 70, Files Expected (lRep+1): 120 FileName /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Trio PatientName Trio_calib_002_run2 Date and time StudyDate 20050905 StudyTime 100821.656000 SeriesTime 104226.748000 AcqTime 104209.522496 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 100 InversionTime -1 RepetitionTime 10100 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 60 IsMosaic 1 ImgPos 1048.1801 1002.6923 -265.4914 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 60 Vc -0.9997 0.0244 0.0005 Vr -0.0238 -0.9764 0.2147 Vs 0.0057 0.2147 0.9767 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID unknown INFO: sorting. INFO: (128 128 60), nframes = 70, ismosaic=1 sdfi->UseSliceScaleFactor 0 datatype = 4, short=4, float=3 Numaris Version: syngo MR 2004A 4VA25A Maj = 4, Min=2, MinMin = 5 Repetition Time = 10100, TR = 10100 ms PE Dir COL COL AutoAlign matrix detected AutoAlign Matrix --------------------- 0.99970 0.02376 -0.00570 -0.49480; -0.02443 0.97638 -0.21466 -40.55519; 0.00047 0.21474 0.97667 12.50291; 0.00000 0.00000 0.00000 1.00000; FileName /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm Identification NumarisVer syngo MR 2004A 4VA25A ScannerModel Trio PatientName Trio_calib_002_run2 Date and time StudyDate 20050905 StudyTime 100821.656000 SeriesTime 104226.748000 AcqTime 104209.522496 Acquisition parameters PulseSeq ep_b0#0 Protocol DIFFUSION_HighRes PhEncDir COL EchoNo 0 FlipAngle 90 EchoTime 100 InversionTime -1 RepetitionTime 10100 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 10 SeriesNo 11 ImageNo 1 NImageRows 1024 NImageCols 1024 NFrames 70 SliceArraylSize 60 IsMosaic 1 ImgPos 131.1612 149.7402 -72.6670 VolRes 2.0000 2.0000 2.0000 VolDim 128 128 60 Vc -0.9997 0.0244 0.0005 Vr -0.0238 -0.9764 0.2147 Vs 0.0057 0.2147 0.9767 VolCenter 0.5005 40.7699 13.4796 TransferSyntaxUID unknown UseSliceScaleFactor 0 (slice 0: 1) IsDWI = 0 sagrev = 1, correv =1, trarev = 0 Vs = 0.0057 0.214665 0.976671 INFO: no Siemens slice order reversal detected (good!). TR=10100.00, TE=100.00, TI=-1.00, flip angle=90.00 i_ras = (-0.999702, 0.0244268, 0.000465598) j_ras = (-0.023757, -0.976382, 0.21474) k_ras = (0.0057, 0.214665, 0.976671) writing to /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz... mri_probedicom --i /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/656000-11-1.dcm > /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dcminfo.dat cp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/gradients.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs cp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/orig/bvalues.txt /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs.tmp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvals.tmp /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals orientLAS /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LPS INFO: input image determinant is 8 mri_convert -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 128 -onk 60 -oid -0.999701 0.0244268 0.000465598 -ojd 0.023757 0.976382 -0.21474 -okd 0.0057 0.214665 0.976671 -oc 0.548018 42.7227 13.0501 -rt nearest /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999701, 0.0244268, 0.000465598) -> (-0.999702, 0.0244268, 0.000465598) normalizing out_j_direction: (0.023757, 0.976382, -0.21474) -> (0.023757, 0.976382, -0.21474) normalizing out_k_direction: (0.0057, 0.214665, 0.976671) -> (0.0057, 0.214665, 0.976671) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.nii.gz... TR=10100.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999701, 0.0244268, 0.000465598) j_ras = (-0.023757, -0.976382, 0.21474) k_ras = (0.0057, 0.214665, 0.976671) Reslicing using nearest writing to /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz... INFO: found /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvals, copying INFO: found /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig.bvecs, converting to LAS mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvecs /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.bvals /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvals eddy_correct /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi_orig_las.nii.gz /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.nii.gz 0 Traceback (most recent call last): File "/usr/local/fsl/bin/imglob", line 11, in <module> load_entry_point('fslpy==1.7.0', 'console_scripts', 'imglob')() File "/usr/local/fsl/fslpython/envs/fslpython/lib/python3.6/site-packages/fsl/scripts/imglob.py", line 109, in main print(' '.join(imgfiles)) UnicodeEncodeError: 'ascii' codec can't encode character '\u0301' in position 32: ordinal not in range(128) Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value mv -f /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs.norot xfmrot /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs.norot /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/bvecs grep: /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog: No such file or directory head: /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog: No such file or directory wc: /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog: open: No such file or directory wc: /Volumes/TOSHIBA_EXT/otros/Académico/Research/image_processing/freesurfer_data_tutorial/diffusion_tutorial/elmo.2005/dmri/dwi.ecclog: open: No such file or directory ERROR: Transform file should be eddy_correct/eddy log file or .mat file Darwin Renes-MacBook-Air-2.local 17.5.0 Darwin Kernel Version 17.5.0: Mon Mar 5 22:24:32 PST 2018; root:xnu-4570.51.1~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Wed Jul 11 17:55:25 CEST 2018

1 0

Zeroes for few regions in 'aparc.a2009s' parcellation.
by vittal korann 11 Jul '18

11 Jul '18

External Email - Use Caution Hello Freesurfer developers, I ran recon-all command to extract all subjects stats. Here I'm mainly targetting the surface area, volume, thickness and mean curve for all subjects. " recon-all -i /filepath/file/ -s /subjectid/ -all " this was the command i used. Now the problem is that I'm getting zeroes for the surface area which is parcellated from 'aparc.a2009s' and it occurred for a large number of subjects. The command for converting stats to .txt is given below: aparcstats2table --hemi lh --subjects 004 008 --parc aparc.a2009s --meas area --tablefile lh.a2009s.area.txt *l**h_G&S_frontomargin_area* *lh_G&S_occipital_inf_area* *lh_G&S_paracentral_area* *lh_G&S_subcentral_area* *lh_G&S_transv_frontopol_area* *lh_G&S_cingulAnt_area* I wanted to know the reason for getting these zeroes. Could anyone plz help me out in this regard. Thanks in advance! *Best* *Vittal*

3 2

Recon-all error: could not set locale
by ?? ? 09 Jul '18

09 Jul '18

External Email - Use Caution Hi Freesurfer Team, I am aware that segmentation of thalamic nuclei is only available in developmental versions of Freesurfer. After I have downloaded the Freesurfer dev version(freesurfer-linux-centos7_x86_64-dev), I get the following error whenever I use the recon-all command: Could not set locale No such file or directory Recon-all works fine when I use the stable 6.0 version. Could anyone tell me how I can fix this problem? Also, I was wondering it is ok to use recon-all from 6.0 version and thalamic nuclei analysis from dev version. Thanks in advance, Kayeong Tak

3 3

Infant atlas/pipeline
by Dominick, Kelli 09 Jul '18

09 Jul '18

External Email - Use Caution Hello Freesurfer Experts, I am hoping to use Freesurfer in infant brain processing. I have looked through the archives and it looks as if there is a beta version developed maybe in 2016 with hopes for wide release soon after. I also saw some attempts to use the UNC templates though not clear if any were successful. Are there still plans to release the infant segmentation through freesurfer? And/or has there been successful used of the UNC templates? Best, Kelli

2 1

questions regarding bias correction prior to Freesurfer processing
by STACEY M SCHAEFER 09 Jul '18

09 Jul '18

External Email - Use Caution Hello Freesurfer experts, Our current 3T T1s exhibit structural hyperintensities due to the inhomogeneity of the receiver coil, but not all scans have hyperintensity issues. The local MRI physicist suggests running N4BiasFieldCorrection through multiple iterations prior to Freesurfer processing on problematic scans. We would like your opinion as to whether running a bias correction on the individual problematic scans could introduce any additional biases in Freesurfer processing. This is a longitudinal sample of ~ 300 participants. Is it OK to run N4BiasFieldCorrection on individual scans as needed? Or would it be better to run the bias correction on all the scans (the entire sample) routinely, even if they do not show hyperintensity issues so all scans are processed similarly across the sample? Or do you have any other suggestions? Your guidance is much appreciated! Thank you. Stacey Stacey M. Schaefer, Ph.D. Center for Healthy Minds University of Wisconsin-Madison 625 W Washington Ave Madison WI 53703 608-263-9321

2 1

niiWrite(): error opening file tmp.nii
by Konstantina Skolariki 09 Jul '18

09 Jul '18

External Email - Use Caution Hi FreeSurfer Developers, I have downloaded freesurfer on my mac and after "setup & configuration” I tried to perform example 1 from "test your FreeSurfer Installation”. However when I type the command, this error message shows up: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from sample-001.mgz... TR=7.25, TE=3.22, TI=600.00, flip angle=7.00 i_ras = (-0, -1, -0) j_ras = (-0, 0, -1) k_ras = (-1, 0, 0) writing to tmp.nii... niiWrite(): error opening file tmp.nii ERROR: failure writing tmp.nii Thanks, Konstantina

3 5

changing label outlines in tksurfer
by Loeffler, Martin 09 Jul '18

09 Jul '18

External Email - Use Caution Dear experts, I’m visualizing a 1st level sig-map together with two specific label files using tksurfer (Freesurfer version 6.0). I’ve extracted those labels before using mri_annotation2label. I would like to change the colours of the label outlines. This is probably a very simple thing to do, but I am somehow stuck and would appreciate any help. Here my code: tksurfer Case01 lh inflated \ -tcl my_script.tcl \ -label-outline \ -label ${label_dir}/lh.label1.label\ -label ${label_dir}/lh.label2.label\ -o ${contrast_dir}/contrast1l/sig.nii.gz with the .tcl file containing the following: labl_set_color 0 0 0 255 labl_set_color 1 0 255 255 make_lateral_view rotate_brain_x -30 redraw Thanks for your help! Martin

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