Freesurfer

freesurfer@nmr.mgh.harvard.edu

4 participants
30090 discussions

Hypointense lesions
by Fotiadis, Panagiotis 07 Jun '13

07 Jun '13

Hi FreeSurfer Community, I was wondering whether there is an automatic tool that outlines the hypointense lesions in a SWI scan. Thank you, Panos

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mri_convert
by Ray, Siddharth 07 Jun '13

07 Jun '13

Hi free-surfer folks, I have some subjects with L-R header flipped in nifti's. Is it possible to flip the header using mri_convert so that I can have the right orientation information for subjects. Please let me know. Thanks, -Siddharth

3 5

FS-FAST - ERROR: mapping surfaces
by preciado＠nmr.mgh.harvard.edu 07 Jun '13

07 Jun '13

I am having an issue when running the preprocess script in fs-fast. It failed once and I tried something and ran the script again and it failed the same way. The command I ran is: preproc-sess -s subj007 -fsd bold -stc siemens -surface fsaverage lhrh -mni305 -fwhm 5 -per-run Below is the part where the error appears to occur, but the full log is attached. Any help would be appreciated. -Ronny 1/1 subj007 1/1 subj007 008 lh --------- Fri Jun 7 10:50:50 EDT 2013 mri_vol2surf --mov /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz --reg /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat --trgsubject fsaverage --interp nearest --projfrac 0.5 --hemi lh --o /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/masks/brain.fsaverage.lh.nii.gz --noreshape --cortex --surfreg sphere.reg srcvol = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/masks/brain.nii.gz srcreg = /autofs/cluster/birn/users/helmer/fMRI_improv/fs-fast/subj007/bold/008/register.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = lh trgsubject = fsaverage surfreg = sphere.reg ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/label/lh.cortex.label Reading surface /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.white Done reading source surface Reading thickness /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 19272 Reading source surface registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/subj007/surf/lh.sphere.reg Done loading source registration surface surf2surf_nnfr(): Vals and Reg dimension mismatch nVals = 157755, nReg 157894 Reading target registration /autofs/cluster/birn/users/helmer/fMRI_improv/freesurfer/subjects/fsaverage/surf/lh.sphere.reg Done loading target registration surface Mapping Surfaces (subj007 -> fsaverage) ERROR: mapping surfaces

3 4

R: Re: R: Re: mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

Ok, now I think that I have downloaded the correct file. I try to rerun trac-all -prep and at the end I'll send you a feedback. Thanks, Stefano ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 7-giu-2013 18.18 A: <stdp82(a)virgilio.it> Cc: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: mris resample: Command not found. This error is permanent after new patch download I dont know why your getting a file named "unknown". If you click this link you should be able to download a file called "mris_resample": ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/ Download it and place it in $FREESURFER_HOME/bin (Usually Applications/freesurfer/bin on Macs). Then make it executable by typing "chmod +x Applications/freesurfer/bin/mris_resample" on the command line. -Zeke If you go this this link On 06/07/2013 12:09 PM, stdp82(a)virgilio.it wrote: > Hi Zeke, thank you very much. > > I have download a file that named "unknown". > > I should rename it as "mris_resample"? > > > Stefano > > ----Messaggio originale---- > Da: zkaufman(a)nmr.mgh.harvard.edu > Data: 7-giu-2013 18.02 > A: <freesurfer(a)nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] mris resample: Command not found. This error is > permanent after new patch download > > Stefano, step 4 should be: > > "chmod +x $FREESURFER_HOME/bin/mris_resample" > > When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need > to see the to see the x's next to mris_resample just like you do with > all the other files in that directory. > > -Zeke > > > On 06/07/2013 11:49 AM, stdp82(a)virgilio.it wrote: > > Hi list, > > > > during trac-all -prep I have this error: > > > > MRISregister() return, current seed 0 > > writing registered surface to > > > /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > > expanding nbhd size to 1 > > mris_resample: Command not found. > > Darwin iMac > > > > I have performed my analysis by the following steps (as recommended by > > Zeke and Lilla): > > > > 1. download "unKnow" file (7.6 MB) at > > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample > > 2. put file in $FREESURFER/bin/ > > 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test > > I did not use this command) > > 5. start trac-all -prep > > 6. ERROR (in inter-reg step) > > > > What's happen? > > > > Thank you very much, > > > > > > Stefano > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > 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 > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > > _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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R: Re: mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

Hi Zeke, thank you very much. I have download a file that named "unknown". I should rename it as "mris_resample"? Stefano ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 7-giu-2013 18.02 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download Stefano, step 4 should be: "chmod +x $FREESURFER_HOME/bin/mris_resample" When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, stdp82(a)virgilio.it wrote: > Hi list, > > during trac-all -prep I have this error: > > MRISregister() return, current seed 0 > writing registered surface to > /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > expanding nbhd size to 1 > mris_resample: Command not found. > Darwin iMac > > I have performed my analysis by the following steps (as recommended by > Zeke and Lilla): > > 1. download "unKnow" file (7.6 MB) at > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample > 2. put file in $FREESURFER/bin/ > 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test > I did not use this command) > 5. start trac-all -prep > 6. ERROR (in inter-reg step) > > What's happen? > > Thank you very much, > > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

2 1

R: Re: mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

[iMac-di-Stefano:/Applications/freesurfer/bin] Stefano% ls -ltotal 4780656-rwxr-xr-x 1 root wheel 60776 Jan 29 00:20 #trac-all#-rwxr-xr-x 1 root wheel 27224 May 14 17:07 4dfptoanalyze-rwxr-xr-x 1 root wheel 12925 May 14 17:07 LongQdecTable.py-rwxr-xr-x@ 1 Stefano wheel 7581520 Jun 6 23:24 Unknown-rwxr-xr-x 1 root wheel 936 May 14 17:07 UpdateNeeded-rwxr-xr-x 1 root wheel 22628 May 14 17:07 analyzeto4dfp-rwxr-xr-x 1 root wheel 7660 May 14 17:07 aparc2feat-rwxr-xr-x 1 root wheel 15795 May 14 17:07 aparcstats2table-rwxr-xr-x 1 root wheel 4657 May 14 17:07 aparcstatsdiff-rwxr-xr-x 1 root wheel 7075840 May 14 17:07 applyMorph-rwxr-xr-x 1 root wheel 8927 May 14 17:07 aseg2feat-rwxr-xr-x 1 root wheel 23702 May 14 17:07 asegstats2table-rwxr-xr-x 1 root wheel 3450 May 14 17:07 asegstatsdiff-rwxr-xr-x 1 root wheel 2087 May 14 17:07 avi2talxfm-rwxr-xr-x 1 root wheel 2209 May 14 17:07 batchjobs-rwxr-xr-x 1 root wheel 5756 May 14 17:07 bblabel-rwxr-xr-x 1 root wheel 24890 May 14 17:07 bbregister-rwxr-xr-x 1 root wheel 14696 May 14 17:07 bedpostx_mgh-rwxr-xr-x 1 root wheel 13268 May 14 17:07 bet.fsl-rwxr-xr-x 1 root wheel 7144 May 14 17:07 beta2sxa-rwxr-xr-x 1 root wheel 7710 May 14 17:07 biasfield-rwxr-xr-x 1 root wheel 417 May 14 17:07 brec-rwxr-xr-x 1 root wheel 973 May 14 17:07 brec.awk-rwxr-xr-x 1 root wheel 10814 May 14 17:07 browse-minc-header.tcl-rwxr-xr-x 1 root wheel 2201 May 14 17:07 bugr-rwxr-xr-x 1 root wheel 1245 May 14 17:07 build_desikan_killiany_gcs.csh-rwxr-xr-x 1 root wheel 75584 May 14 17:07 check_siemens_dir-rwxr-xr-x 1 root wheel 2496 May 14 17:07 check_subject-rwxr-xr-x 1 root wheel 1113 May 14 17:07 clear_fs_env.csh-rwxr-xr-x 1 root wheel 4458 May 14 17:07 compute_interrater_variability.csh-rwxr-xr-x 1 root wheel 4490 May 14 17:07 compute_label_volumes.csh-rwxr-xr-x 1 root wheel 214788 May 14 17:07 compute_vox2vox-rwxr-xr-x 1 root wheel 6389728 May 14 17:07 connectgraph-rwxr-xr-x 1 root wheel 6776500 May 14 17:07 conv1d_test-rwxr-xr-x 1 root wheel 7133948 May 14 17:07 conv1d_test_cuda-rwxr-xr-x 1 root wheel 6794716 May 14 17:07 convgaussian_test-rwxr-xr-x 1 root wheel 7119796 May 14 17:07 convgaussian_test_cuda-rwxr-xr-x 1 root wheel 1010 May 14 17:07 cor_to_minc-rwxr-xr-x 1 root wheel 4378 May 14 17:07 cp-dicom-rwxr-xr-x 1 root wheel 6893596 May 14 17:07 createMorph-rwxr-xr-x 1 root wheel 1851 May 14 17:07 cuda_setup-rwxr-xr-x 1 root wheel 76 May 14 17:07 cudadetect-rwxr-xr-x 1 root wheel 13308 May 14 17:07 cudadetect.bin-rwxr-xr-x 1 root wheel 12100 May 14 17:07 datastruct_utils.py-rwxr-xr-x 1 root wheel 6122 May 14 17:07 dcmdir-info-mgh-rwxr-xr-x 1 root wheel 23416 May 14 17:07 dcmunpack-rwxr-xr-x 1 root wheel 938 May 14 17:07 deface_subject-rwxr-xr-x 1 root wheel 8865 May 14 17:07 defect-seg-rwxr-xr-x 1 root wheel 4616 May 14 17:07 dicom-rename-rwxr-xr-x 1 root wheel 6452672 May 14 17:07 dmri_mergepaths-rwxr-xr-x 1 root wheel 6651560 May 14 17:07 dmri_paths-rwxr-xr-x 1 root wheel 6545252 May 14 17:07 dmri_pathstats-rwxr-xr-x 1 root wheel 6460264 May 14 17:07 dmri_spline-rwxr-xr-x 1 root wheel 6525716 May 14 17:07 dmri_tensoreig-rwxr-xr-x 1 root wheel 6660692 May 14 17:07 dmri_train-rwxr-xr-x 1 root wheel 6519924 May 14 17:07 dmri_trk2trk-rwxr-xr-x 1 root wheel 6501728 May 14 17:07 dmri_vox2vox-rwxr-xr-x 1 root wheel 6265 May 14 17:07 dmrirc.example-rwxr-xr-x 1 root wheel 7361 May 14 17:07 dmrirc.long.example-rwxr-xr-x 1 root wheel 20888 May 14 17:07 dsh-rwxr-xr-x 1 root wheel 14691 May 14 17:07 dt_recon-rwxr-xr-x 1 root wheel 31462 May 14 17:07 epidewarp.fsl-rwxr-xr-x 1 root wheel 6944772 May 14 17:07 exportGcam-rwxr-xr-x 1 root wheel 313 May 14 17:07 extract_talairach_avi_QA.awk-rwxr-xr-x 1 root wheel 8070 May 14 17:07 feat2segstats-rwxr-xr-x 1 root wheel 12563 May 14 17:07 feat2surf-rwxr-xr-x 1 root wheel 581 May 14 17:07 findsession-rwxr-xr-x 1 root wheel 756 May 14 17:07 fix_subject-rwxr-xr-x 1 root wheel 1114 May 14 17:07 fix_subject-lh-rwxr-xr-x 1 root wheel 1114 May 14 17:07 fix_subject-rh-rwxr-xr-x 1 root wheel 731 May 14 17:07 fix_subject_corrected-rwxr-xr-x 1 root wheel 1447 May 14 17:07 fix_subject_corrected-lh-rwxr-xr-x 1 root wheel 1358 May 14 17:07 fix_subject_corrected-rh-rwxr-xr-x 1 root wheel 952 May 14 17:07 fix_subject_on_seychelles-rwxr-xr-x 1 root wheel 3369 May 14 17:07 fixup_mni_paths-rwxr-xr-x 1 root wheel 5781 May 14 17:07 flip4fsl-rwxr-xr-x 1 root wheel 23072 May 14 17:07 flip_4dfp-rwxr-xr-x 1 root wheel 9859960 May 14 17:07 flirt.fsl-rw-r--r-- 1 root wheel 2919 May 14 17:07 flirt.newdefault.20080811.sch-rwxr-xr-x 1 root wheel 1408 May 14 17:07 fname2ext-rwxr-xr-x 1 root wheel 1438 May 14 17:07 fname2stem-rwxr-xr-x 1 root wheel 855 May 14 17:07 freesurfer-rwxr-xr-x 1 root wheel 184 May 14 17:07 freeview-rwxr-xr-x 1 root wheel 445424 May 14 17:07 fsPrintHelp-rwxr-xr-x 1 root wheel 4352 May 14 17:07 fs_lib_check-rwxr-xr-x 1 root wheel 635 May 14 17:07 fs_time-rwxr-xr-x 1 root wheel 7691 May 14 17:07 fscalc-rwxr-xr-x 1 root wheel 5794 May 14 17:07 fscalc.fsl-rwxr-xr-x 1 root wheel 138 May 14 17:07 fsfget-rwxr-xr-x 1 root wheel 4391 May 14 17:07 fsfget.tcl-rwxr-xr-x 1 root wheel 2815 May 14 17:07 fsgd_parser.py-rwxr-xr-x 1 root wheel 445424 May 14 17:07 fshelp-rwxr-xr-x 1 root wheel 6368760 May 14 17:08 fsl_label2voxel-rwxr-xr-x 1 root wheel 15462 May 14 17:08 fsl_rigid_register-rwxr-xr-x 1 root wheel 16491 May 14 17:08 fsl_sub_mgh-rwxr-xr-x 1 root wheel 11157384 May 14 17:08 fslmaths.fsl-rwxr-xr-x 1 root wheel 8657972 May 14 17:08 fslorient.fsl-rwxr-xr-x 1 root wheel 20703 May 14 17:08 fslregister-rwxr-xr-x 1 root wheel 5964 May 14 17:08 fslswapdim.fsl-rwxr-xr-x 1 root wheel 445424 May 14 17:08 fsman-rwxr-xr-x 1 root wheel 1340 May 14 17:08 fsr-checkxopts-rwxr-xr-x 1 root wheel 1479 May 14 17:08 fsr-getxopts-rwxr-xr-x 1 root wheel 14608 May 14 17:08 fsutils.py-rwxr-xr-x 1 root wheel 236204 May 14 17:08 gauss_4dfp-rwxr-xr-x 1 root wheel 1069708 May 14 17:08 gca_read_test-rwxr-xr-x 1 root wheel 449800 May 14 17:08 gcamCompare-rwxr-xr-x 1 root wheel 1133256 May 14 17:08 gcam_addstatus_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_addstatus_test_cuda-rwxr-xr-x 1 root wheel 1167736 May 14 17:08 gcam_applygradient_test-rwxr-xr-x 1 root wheel 1266424 May 14 17:08 gcam_applygradient_test_cuda-rwxr-xr-x 1 root wheel 1092372 May 14 17:08 gcam_clear_test-rwxr-xr-x 1 root wheel 1217244 May 14 17:08 gcam_clear_test_cuda-rwxr-xr-x 1 root wheel 1101124 May 14 17:08 gcam_cmp_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_cmp_test_cuda-rwxr-xr-x 1 root wheel 6710676 May 14 17:08 gcam_jacobenergy_test-rwxr-xr-x 1 root wheel 818352 May 14 17:08 gcam_jacobenergy_test_cuda-rwxr-xr-x 1 root wheel 1146064 May 14 17:08 gcam_jacobterm_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_jacobterm_test_cuda-rwxr-xr-x 1 root wheel 1064196 May 14 17:08 gcam_labelenergy_test-rwxr-xr-x 1 root wheel 818328 May 14 17:08 gcam_labelenergy_test_cuda-rwxr-xr-x 1 root wheel 6784284 May 14 17:08 gcam_labelterm_copydeltas_test-rwxr-xr-x 1 root wheel 822472 May 14 17:08 gcam_labelterm_copydeltas_test_cuda-rwxr-xr-x 1 root wheel 6784284 May 14 17:08 gcam_labelterm_final_test-rwxr-xr-x 1 root wheel 822472 May 14 17:08 gcam_labelterm_final_test_cuda-rwxr-xr-x 1 root wheel 6897540 May 14 17:08 gcam_labelterm_mainloop_test-rwxr-xr-x 1 root wheel 822528 May 14 17:08 gcam_labelterm_mainloop_test_cuda-rwxr-xr-x 1 root wheel 6802372 May 14 17:08 gcam_labelterm_postantconsist_test-rwxr-xr-x 1 root wheel 822496 May 14 17:08 gcam_labelterm_postantconsist_test_cuda-rwxr-xr-x 1 root wheel 6869460 May 14 17:08 gcam_labelterm_removeoutliers_test-rwxr-xr-x 1 root wheel 822296 May 14 17:08 gcam_labelterm_removeoutliers_test_cuda-rwxr-xr-x 1 root wheel 6910236 May 14 17:08 gcam_labelterm_test-rwxr-xr-x 1 root wheel 822504 May 14 17:08 gcam_labelterm_test_cuda-rwxr-xr-x 1 root wheel 6735988 May 14 17:08 gcam_lle_test-rwxr-xr-x 1 root wheel 818352 May 14 17:08 gcam_lle_test_cuda-rwxr-xr-x 1 root wheel 6792924 May 14 17:08 gcam_llterm_test-rwxr-xr-x 1 root wheel 822504 May 14 17:08 gcam_llterm_test_cuda-rwxr-xr-x 1 root wheel 6871988 May 14 17:08 gcam_removesingularities_test-rwxr-xr-x 1 root wheel 1266080 May 14 17:08 gcam_removesingularities_test_cuda-rwxr-xr-x 1 root wheel 1133256 May 14 17:08 gcam_removestatus_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_removestatus_test_cuda-rwxr-xr-x 1 root wheel 6867788 May 14 17:08 gcam_smoothgradient_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_smoothgradient_test_cuda-rwxr-xr-x 1 root wheel 1064212 May 14 17:08 gcam_smoothnessenergy_test-rwxr-xr-x 1 root wheel 818328 May 14 17:08 gcam_smoothnessenergy_test_cuda-rwxr-xr-x 1 root wheel 1137616 May 14 17:08 gcam_smoothnessterm_test-rwxr-xr-x 1 root wheel 818320 May 14 17:08 gcam_smoothnessterm_test_cuda-rwxr-xr-x 1 root wheel 1092340 May 14 17:08 gcam_undogradient_test-rwxr-xr-x 1 root wheel 1217244 May 14 17:08 gcam_undogradient_test_cuda-rwxr-xr-x 1 root wheel 1092260 May 14 17:08 gcam_write_test-rwxr-xr-x 1 root wheel 1403736 May 14 17:08 gcam_write_test_cuda-rwxr-xr-x 1 root wheel 783 May 14 17:08 get_label_thickness-rwxr-xr-x 1 root wheel 968 May 14 17:08 getfullpath-rwxr-xr-x 1 root wheel 205384 May 14 17:08 gifti_test-rwxr-xr-x 1 root wheel 280720 May 14 17:08 gifti_tool-rwxr-xr-x 1 root wheel 16812 May 14 17:08 grad_unwarp-rwxr-xr-x 1 root wheel 228 May 14 17:08 help_xml_validate-rwxr-xr-x 1 root wheel 6668372 May 14 17:08 hiam_make_surfaces-rwxr-xr-x 1 root wheel 6723212 May 14 17:08 hiam_make_template-rwxr-xr-x 1 root wheel 6839244 May 14 17:08 hiam_register-rwxr-xr-x 1 root wheel 6470716 May 14 17:08 histo_compute_joint_density-rwxr-xr-x 1 root wheel 6449756 May 14 17:08 histo_fix_topology-rwxr-xr-x 1 root wheel 6557828 May 14 17:08 histo_register_block-rwxr-xr-x 1 root wheel 6449748 May 14 17:08 histo_segment-rwxr-xr-x 1 root wheel 6462572 May 14 17:08 histo_synthesize-rwxr-xr-x 1 root wheel 13344 May 14 17:08 ico_supersample-rw-r--r-- 1 root wheel 128 May 14 17:08 id.xfm-rwxr-xr-x 1 root wheel 18444 May 14 17:08 ifh2hdr-rwxr-xr-x 1 root wheel 260684 May 14 17:08 imgreg_4dfp-rwxr-xr-x 1 root wheel 993 May 14 17:08 inflate_subject-rwxr-xr-x 1 root wheel 979 May 14 17:08 inflate_subject-lh-rwxr-xr-x 1 root wheel 978 May 14 17:08 inflate_subject-rh-rwxr-xr-x 1 root wheel 1080 May 14 17:08 inflate_subject3-rwxr-xr-x 1 root wheel 1050 May 14 17:08 inflate_subject_new-rwxr-xr-x 1 root wheel 992 May 14 17:08 inflate_subject_new-lh-rwxr-xr-x 1 root wheel 995 May 14 17:08 inflate_subject_new-rh-rwxr-xr-x 1 root wheel 1060 May 14 17:08 inflate_subject_sc-rwxr-xr-x 1 root wheel 1857 May 14 17:08 is-surface-rwxr-xr-x 1 root wheel 1133 May 14 17:08 isanalyze-rwxr-xr-x 1 root wheel 1377 May 14 17:08 isnifti-rw-------@ 1 Stefano wheel 46574724 Mar 22 20:48 kvl.zip-rwxr-xr-x 1 root wheel 5059016 May 14 17:08 kvlAddBorder-rwxr-xr-x 1 root wheel 386448 May 14 17:08 kvlAddMeshToMeshCollection-rwxr-xr-x 1 root wheel 5123480 May 14 17:08 kvlAddProbabilityImages-rwxr-xr-x 1 root wheel 5776276 May 14 17:08 kvlApplyTransform-rwxr-xr-x 1 root wheel 5054592 May 14 17:08 kvlAugmentManualSegmentationWithAutomatedSegmentation-rwxr-xr-x 1 root wheel 5269008 May 14 17:08 kvlAutoCrop-rwxr-xr-x 1 root wheel 5233008 May 14 17:09 kvlBinaryThresholdImage-rwxr-xr-x 1 root wheel 5458048 May 14 17:09 kvlCalculateAtlasMeshCollectionTotalCost-rwxr-xr-x 1 root wheel 5410272 May 14 17:09 kvlCalculatePositionCost-rwxr-xr-x 1 root wheel 386576 May 14 17:09 kvlChangeKOfMeshCollection-rwxr-xr-x 1 root wheel 386576 May 14 17:09 kvlChangePointParametersOfMeshCollection-rwxr-xr-x 1 root wheel 5141260 May 14 17:09 kvlColorCodeProbabilityImages-rwxr-xr-x 1 root wheel 5054592 May 14 17:09 kvlCombineManualSegmentationProtocols-rwxr-xr-x 1 root wheel 5147652 May 14 17:09 kvlCompressImage-rwxr-xr-x 1 root wheel 5099284 May 14 17:09 kvlConvert-rwxr-xr-x 1 root wheel 5054592 May 14 17:09 kvlCorrectLeftSideLabelsToRightSideLabels-rwxr-xr-x 1 root wheel 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mri_probedicom-rwxr-xr-x 1 root wheel 6445900 May 14 17:13 mri_reduce-rwxr-xr-x 1 root wheel 7036844 May 14 17:13 mri_register-rwxr-xr-x 1 root wheel 6525564 May 14 17:13 mri_relabel_hypointensities-rwxr-xr-x 1 root wheel 6957376 May 14 17:13 mri_remove_neck-rwxr-xr-x 1 root wheel 5288 May 14 17:13 mri_reorient_LR.csh-rwxr-xr-x 1 root wheel 6530000 May 14 17:13 mri_ribbon-rwxr-xr-x 1 root wheel 6504324 May 14 17:13 mri_rigid_register-rwxr-xr-x 1 root wheel 7341236 May 14 17:13 mri_robust_register-rwxr-xr-x 1 root wheel 7301884 May 14 17:13 mri_robust_template-rwxr-xr-x 1 root wheel 6442036 May 14 17:13 mri_seg_diff-rwxr-xr-x 1 root wheel 6442076 May 14 17:13 mri_seghead-rwxr-xr-x 1 root wheel 6974232 May 14 17:13 mri_segment-rwxr-xr-x 1 root wheel 6533804 May 14 17:13 mri_segment_wm_damage-rwxr-xr-x 1 root wheel 6648860 May 14 17:13 mri_segreg-rwxr-xr-x 1 root wheel 7046720 May 14 17:13 mri_segstats-rwxr-xr-x 1 root wheel 7353352 May 14 17:13 mri_segstats_cuda-rwxr-xr-x 1 root wheel 6454188 May 14 17:13 mri_simulate_atrophy-rwxr-xr-x 1 root wheel 6525940 May 14 17:13 mri_stats2seg-rwxr-xr-x 1 root wheel 6458268 May 14 17:13 mri_strip_nonwhite-rwxr-xr-x 1 root wheel 516476 May 14 17:13 mri_strip_subject_info-rwxr-xr-x 1 root wheel 6627844 May 14 17:13 mri_surf2surf-rwxr-xr-x 1 root wheel 6542764 May 14 17:13 mri_surf2vol-rwxr-xr-x 1 root wheel 6510976 May 14 17:13 mri_surfacemask-rwxr-xr-x 1 root wheel 6607172 May 14 17:13 mri_surfcluster-rwxr-xr-x 1 root wheel 6470652 May 14 17:13 mri_synthesize-rwxr-xr-x 1 root wheel 6827544 May 14 17:13 mri_tessellate-rwxr-xr-x 1 root wheel 6445612 May 14 17:14 mri_threshold-rwxr-xr-x 1 root wheel 6758728 May 14 17:14 mri_topologycorrection-rwxr-xr-x 1 root wheel 6580628 May 14 17:14 mri_train-rwxr-xr-x 1 root wheel 6558716 May 14 17:14 mri_transform-rwxr-xr-x 1 root wheel 6504476 May 14 17:14 mri_transform_to_COR-rwxr-xr-x 1 root wheel 6587796 May 14 17:14 mri_twoclass-rwxr-xr-x 1 root wheel 6364536 May 14 17:14 mri_validate_skull_stripped-rwxr-xr-x 1 root wheel 6492756 May 14 17:14 mri_vol2roi-rwxr-xr-x 1 root wheel 6638532 May 14 17:14 mri_vol2surf-rwxr-xr-x 1 root wheel 6773820 May 14 17:14 mri_vol2vol-rwxr-xr-x 1 root wheel 7150812 May 14 17:14 mri_vol2vol_cuda-rwxr-xr-x 1 root wheel 6552924 May 14 17:14 mri_volcluster-rwxr-xr-x 1 root wheel 6375312 May 14 17:14 mri_voldiff-rwxr-xr-x 1 root wheel 6573060 May 14 17:14 mri_volsynth-rwxr-xr-x 1 root wheel 7275164 May 14 17:14 mri_watershed-rwxr-xr-x 1 root wheel 6441600 May 14 17:14 mri_wmfilter-rwxr-xr-x 1 root wheel 6437708 May 14 17:14 mri_xvolavg-rwxr-xr-x 1 root wheel 6459100 May 14 17:14 mri_z2p-rwxr-xr-x 1 root wheel 6768388 May 14 17:14 mris2rgb-rwxr-xr-x 1 root wheel 6835564 May 14 17:14 mris_AA_shrinkwrap-rwxr-xr-x 1 root wheel 6470836 May 14 17:14 mris_BA_segment-rwxr-xr-x 1 root wheel 6559596 May 14 17:14 mris_add_template-rwxr-xr-x 1 root wheel 7024640 May 14 17:14 mris_anatomical_stats-rwxr-xr-x 1 root wheel 6521684 May 14 17:14 mris_annot_to_segmentation-rwxr-xr-x 1 root wheel 6962328 May 14 17:14 mris_apply_reg-rwxr-xr-x 1 root wheel 6580156 May 14 17:14 mris_aseg_distance-rwxr-xr-x 1 root wheel 6537860 May 14 17:14 mris_average_curvature-rwxr-xr-x 1 root wheel 6462580 May 14 17:14 mris_average_parcellation-rwxr-xr-x 1 root wheel 7044292 May 14 17:14 mris_ca_deform-rwxr-xr-x 1 root wheel 7042168 May 14 17:14 mris_ca_label-rwxr-xr-x 1 root wheel 6593180 May 14 17:14 mris_ca_train-rwxr-xr-x 1 root wheel 6924184 May 14 17:14 mris_calc-rwxr-xr-x 1 root wheel 6575532 May 14 17:14 mris_classify_thickness-rwxr-xr-x 1 root wheel 6558876 May 14 17:14 mris_compute_acorr-rwxr-xr-x 1 root wheel 11414 May 14 17:14 mris_compute_lgi-rwxr-xr-x 1 root wheel 6458212 May 14 17:14 mris_compute_optimal_kernel-rwxr-xr-x 1 root wheel 6458500 May 14 17:14 mris_compute_overlap-rwxr-xr-x 1 root wheel 6478784 May 14 17:15 mris_compute_parc_overlap-rwxr-xr-x 1 root wheel 6681380 May 14 17:15 mris_congeal-rwxr-xr-x 1 root wheel 6655460 May 14 17:15 mris_convert-rwxr-xr-x 1 root wheel 7075312 May 14 17:15 mris_curvature-rwxr-xr-x 1 root wheel 6681628 May 14 17:15 mris_curvature_stats-rwxr-xr-x 1 root wheel 7059836 May 14 17:15 mris_deform-rwxr-xr-x 1 root wheel 6533908 May 14 17:15 mris_density-rwxr-xr-x 1 root wheel 6533604 May 14 17:15 mris_diff-rwxr-xr-x 1 root wheel 6516924 May 14 17:15 mris_distance_map-rwxr-xr-x 1 root wheel 6557252 May 14 17:15 mris_distance_to_label-rwxr-xr-x 1 root wheel 6622540 May 14 17:15 mris_distance_transform-rwxr-xr-x 1 root wheel 6550828 May 14 17:15 mris_divide_parcellation-rwxr-xr-x 1 root wheel 6458332 May 14 17:15 mris_entropy-rwxr-xr-x 1 root wheel 6626300 May 14 17:15 mris_errors-rwxr-xr-x 1 root wheel 6898552 May 14 17:15 mris_euler_number-rwxr-xr-x 1 root wheel 6851748 May 14 17:15 mris_expand-rwxr-xr-x 1 root wheel 6919364 May 14 17:15 mris_extract_main_component-rwxr-xr-x 1 root wheel 6876788 May 14 17:15 mris_exvivo_surfaces-rwxr-xr-x 1 root wheel 80480 May 14 17:15 mris_fbirn_annot-rwxr-xr-x 1 root wheel 6558764 May 14 17:15 mris_fill-rwxr-xr-x 1 root wheel 6521132 May 14 17:15 mris_find_flat_regions-rwxr-xr-x 1 root wheel 7278632 May 14 17:15 mris_fix_topology-rwxr-xr-x 1 root wheel 7580576 May 14 17:15 mris_fix_topology_cuda-rwxr-xr-x 1 root wheel 6885188 May 14 17:15 mris_flatten-rwxr-xr-x 1 root wheel 7290920 May 14 17:15 mris_flatten_cuda-rwxr-xr-x 1 root wheel 6547416 May 14 17:15 mris_fwhm-rwxr-xr-x 1 root wheel 6467036 May 14 17:15 mris_hausdorff_dist-rwxr-xr-x 1 root wheel 7218296 May 14 17:15 mris_inflate-rwxr-xr-x 1 root wheel 7524336 May 14 17:15 mris_inflate_cuda-rwxr-xr-x 1 root wheel 6479960 May 14 17:15 mris_info-rwxr-xr-x 1 root wheel 6722908 May 14 17:15 mris_intensity_profile-rwxr-xr-x 1 root wheel 6961568 May 14 17:15 mris_jacobian-rwxr-xr-x 1 root wheel 6534228 May 14 17:15 mris_label2annot-rwxr-xr-x 1 root wheel 6458500 May 14 17:15 mris_label_area-rwxr-xr-x 1 root wheel 6460176 May 14 17:16 mris_label_calc-rwxr-xr-x 1 root wheel 6458212 May 14 17:16 mris_label_mode-rwxr-xr-x 1 root wheel 6898060 May 14 17:16 mris_longitudinal_surfaces-rwxr-xr-x 1 root wheel 6608980 May 14 17:16 mris_make_average_surface-rwxr-xr-x 1 root wheel 6567444 May 14 17:16 mris_make_face_parcellation-rwxr-xr-x 1 root wheel 7414288 May 14 17:16 mris_make_surfaces-rwxr-xr-x 1 root wheel 6847940 May 14 17:16 mris_make_template-rwxr-xr-x 1 root wheel 6555500 May 14 17:16 mris_map_cuts-rwxr-xr-x 1 root wheel 6843572 May 14 17:16 mris_mef_surfaces-rwxr-xr-x 1 root wheel 6466708 May 14 17:16 mris_merge_parcellations-rwxr-xr-x 1 root wheel 6525476 May 14 17:16 mris_morph_stats-rwxr-xr-x 1 root wheel 6897412 May 14 17:16 mris_ms_refine-rwxr-xr-x 1 root wheel 6542300 May 14 17:16 mris_ms_surface_CNR-rwxr-xr-x 1 root wheel 6563100 May 14 17:16 mris_multiscale_stats-rwxr-xr-x 1 root wheel 6475252 May 14 17:16 mris_niters2fwhm-rwxr-xr-x 1 root wheel 6797844 May 14 17:16 mris_nudge-rwxr-xr-x 1 root wheel 543056 May 14 17:16 mris_parcellate_connectivity-rwxr-xr-x 1 root wheel 7232156 May 14 17:16 mris_pmake-rwxr-xr-x 1 root wheel 39591 May 14 17:16 mris_preproc-rwxr-xr-x 1 root wheel 6893956 May 14 17:16 mris_refine_surfaces-rwxr-xr-x 1 root wheel 7351544 May 14 17:16 mris_register-rwxr-xr-x 1 root wheel 6739604 May 14 17:16 mris_register_to_volume-rwxr-xr-x 1 root wheel 6936400 May 14 17:16 mris_remove_intersection-rwxr-xr-x 1 root wheel 6504668 May 14 17:16 mris_remove_negative_vertices-rwxr-xr-x 1 root wheel 6525444 May 14 17:16 mris_remove_variance-rwxr-xr-x 1 root wheel 6483444 May 14 17:16 mris_rescale-rwxr-xr-x 1 root wheel 6571900 May 14 17:16 mris_reverse-rwxr-xr-x 1 root wheel 7637 May 14 17:16 mris_roiCircle-rwxr-xr-x 1 root wheel 6487692 May 14 17:16 mris_rotate-rwxr-xr-x 1 root wheel 6471124 May 14 17:16 mris_sample_label-rwxr-xr-x 1 root wheel 6580092 May 14 17:16 mris_sample_parc-rwxr-xr-x 1 root wheel 6454884 May 14 17:16 mris_seg2annot-rwxr-xr-x 1 root wheel 6525508 May 14 17:16 mris_segment_vals-rwxr-xr-x 1 root wheel 6732396 May 14 17:16 mris_show-rwxr-xr-x 1 root wheel 6839588 May 14 17:16 mris_shrinkwrap-rwxr-xr-x 1 root wheel 7104880 May 14 17:16 mris_smooth-rwxr-xr-x 1 root wheel 7355672 May 14 17:16 mris_sphere-rwxr-xr-x 1 root wheel 7749348 May 14 17:17 mris_sphere_cuda-rwxr-xr-x 1 root wheel 6597364 May 14 17:17 mris_spherical_average-rwxr-xr-x 1 root wheel 6521204 May 14 17:17 mris_surface_change-rwxr-xr-x 1 root wheel 6542156 May 14 17:17 mris_surface_stats-rwxr-xr-x 1 root wheel 6475332 May 14 17:17 mris_surface_to_vol_distances-rwxr-xr-x 1 root wheel 6487980 May 14 17:17 mris_svm_classify-rwxr-xr-x 1 root wheel 6554788 May 14 17:17 mris_svm_train-rwxr-xr-x 1 root wheel 6483508 May 14 17:17 mris_talairach-rwxr-xr-x 1 root wheel 6868788 May 14 17:17 mris_thickness-rwxr-xr-x 1 root wheel 6462524 May 14 17:17 mris_thickness_comparison-rwxr-xr-x 1 root wheel 6609020 May 14 17:17 mris_thickness_diff-rwxr-xr-x 1 root wheel 6793844 May 14 17:17 mris_topo_fixer-rwxr-xr-x 1 root wheel 6587956 May 14 17:17 mris_transform-rwxr-xr-x 1 root wheel 6458356 May 14 17:17 mris_translate_annotation-rwxr-xr-x 1 root wheel 6571324 May 14 17:17 mris_twoclass-rwxr-xr-x 1 root wheel 7048064 May 14 17:17 mris_volmask-rwxr-xr-x 1 root wheel 7024080 May 14 17:17 mris_volmask_novtk-rwxr-xr-x 1 root wheel 81 May 14 17:17 mris_volmask_vtk-rwxr-xr-x 1 root wheel 7008888 May 14 17:17 mris_volmask_vtk.bin-rwxr-xr-x 1 root wheel 11555 May 14 17:17 mris_volsmooth-rwxr-xr-x 1 root wheel 6454212 May 14 17:17 mris_volume-rwxr-xr-x 1 root wheel 6525444 May 14 17:17 mris_w_to_curv-rwxr-xr-x 1 root wheel 6529676 May 14 17:17 mris_wm_volume-rwxr-xr-x 1 root wheel 7058520 May 14 17:17 mrisp_paint-rwxr-xr-x 1 root wheel 927 May 14 17:17 ms_refine_subject-rwxr-xr-x 1 root wheel 361548 May 14 17:17 nmovie-rwxr-xr-x 1 root wheel 171716 May 14 17:17 optseq2-rwxr-xr-x 1 root wheel 15570 May 14 17:17 parc_atlas_jackknife_test-rwxr-xr-x 1 root wheel 8818 May 14 17:17 pctsurfcon-rwxr-xr-x 1 root wheel 2283 May 14 17:17 petsc_setup-rwxr-xr-x 1 root wheel 22465 May 14 17:17 plot_structure_stats.tcl-rwxr-xr-x 1 root wheel 4323 May 14 17:17 predict_v1.sh-rwxr-xr-x 1 root wheel 26812 May 14 17:17 progressbar.tcl-rwxr-xr-x 1 root wheel 259 May 14 17:17 qdec-rwxr-xr-x 1 root wheel 8733444 May 14 17:17 qdec.bin-rwxr-xr-x 1 root wheel 658640 May 14 17:17 qdec_glmfit-rwxr-xr-x 1 root wheel 1764 May 14 17:17 qt_setup-rwxr-xr-x 1 root wheel 209408 May 14 17:17 rbftest-rwxr-xr-x 1 root wheel 7611 May 14 17:17 rcbf-prep-rwxr-xr-x 1 root wheel 15908 May 14 17:17 rebuild_gca_atlas.csh-rwxr-xr-x 1 root wheel 268538 May 14 17:17 recon-all-rwxr-xr-x 1 root wheel 23095 May 14 17:17 recon-all.makefile-rwxr-xr-x 1 root wheel 22846 May 14 17:17 reg-feat2anat-rwxr-xr-x 1 root wheel 4341 May 14 17:17 reg-mni305.2mm-rwxr-xr-x 1 root wheel 6376400 May 14 17:17 regdat2xfm-rwxr-xr-x 1 root wheel 2503 May 14 17:17 register.csh-rwxr-xr-x 1 root wheel 972 May 14 17:17 register_child-rwxr-xr-x 1 root wheel 1106 May 14 17:17 register_elderly_subject-rwxr-xr-x 1 root wheel 971 May 14 17:17 register_subject-rwxr-xr-x 1 root wheel 967 May 14 17:17 register_subject_flash-rwxr-xr-x 1 root wheel 986 May 14 17:17 register_subject_mixed-rwxr-xr-x 1 root wheel 763 May 14 17:17 reinflate_subject-rwxr-xr-x 1 root wheel 931 May 14 17:17 reinflate_subject-lh-rwxr-xr-x 1 root wheel 931 May 14 17:17 reinflate_subject-rh-rwxr-xr-x 1 root wheel 993 May 14 17:17 remove_talairach-rwxr-xr-x 1 root wheel 763 May 14 17:17 renormalize_T1_subject-rwxr-xr-x 1 root wheel 788 May 14 17:17 renormalize_subject-rwxr-xr-x 1 root wheel 1002 May 14 17:17 renormalize_subject_keep_editting-rwxr-xr-x 1 root wheel 75392 May 14 17:17 repair_siemens_file-rwxr-xr-x 1 root wheel 948 May 14 17:17 reregister_subject_mixed-rwxr-xr-x 1 root wheel 9158 May 14 17:17 rtview-rwxr-xr-x 1 root wheel 6291 May 14 17:17 run-qdec-glm-rwxr-xr-x 1 root wheel 3732 May 14 17:17 run_mris_preproc-rwxr-xr-x 1 root wheel 1676 May 14 17:17 segment_monkey-rwxr-xr-x 1 root wheel 1443 May 14 17:17 segment_subject-rwxr-xr-x 1 root wheel 1732 May 14 17:17 segment_subject_notal-rwxr-xr-x 1 root wheel 1545 May 14 17:17 segment_subject_notal2-rwxr-xr-x 1 root wheel 1516 May 14 17:17 segment_subject_old_skull_strip-rwxr-xr-x 1 root wheel 1585 May 14 17:17 segment_subject_sc-rwxr-xr-x 1 root wheel 1599 May 14 17:17 segment_subject_talmgh-rwxr-xr-x 1 root wheel 3330 May 14 17:17 setlabelstat-rwxr-xr-x 1 root wheel 10224 May 14 17:17 sfa2fieldsign-rwxr-xr-x 1 root wheel 774 May 14 17:17 show_tal-rwxr-xr-x 1 root wheel 220 May 14 17:17 skip_long_make_checks-rwxr-xr-x 1 root wheel 8771600 May 14 17:17 slicetimer.fsl-rwxr-xr-x 1 root wheel 707 May 14 17:17 sphere_subject-rwxr-xr-x 1 root wheel 882 May 14 17:17 sphere_subject-lh-rwxr-xr-x 1 root wheel 881 May 14 17:17 sphere_subject-rh-rwxr-xr-x 1 root wheel 6558884 May 14 17:17 spherical_stats-rwxr-xr-x 1 root wheel 1802 May 14 17:17 spm_t_to_b-rwxr-xr-x 1 root wheel 5922 May 14 17:17 spmmat2register-rwxr-xr-x 1 root wheel 21612 May 14 17:17 spmregister-rwxr-xr-x 1 root wheel 2455 May 14 17:17 sratio-rwxr-xr-x 1 root wheel 6554748 May 14 17:17 stat_normalize-rwxr-xr-x 1 root wheel 1829 May 14 17:17 stem2fname-rwxr-xr-x 1 root wheel 8756 May 14 17:17 stim_polar-rwxr-xr-x 1 root wheel 556 May 14 17:17 subject_info.py-rwxr-xr-x 1 root wheel 10583672 May 14 17:17 surf2vol-rwxr-xr-x 1 root wheel 7698 May 14 17:17 surfreg-rwxr-xr-x 1 root wheel 1494 May 14 17:17 t4img_4dfp-rwxr-xr-x 1 root wheel 265468 May 14 17:17 t4imgs_4dfp-rwxr-xr-x 1 root wheel 1049 May 14 17:17 tal_QC_AZS-rwxr-xr-x 1 root wheel 856 May 14 17:17 tal_compare-rwxr-xr-x 1 root wheel 5185 May 14 17:17 talairach-rwxr-xr-x 1 root wheel 3115 May 14 17:17 talairach2-rwxr-xr-x 1 root wheel 6835816 May 14 17:17 talairach_afd-rwxr-xr-x 1 root wheel 5387 May 14 17:17 talairach_avi-rwxr-xr-x 1 root wheel 1132 May 14 17:17 talairach_mgh-rwxr-xr-x 1 root wheel 14605 May 14 17:17 talsegprob-rwxr-xr-x 1 root wheel 2405 May 14 17:17 tcl_setup-rwxr-xr-x 1 root wheel 10407 May 14 17:17 test_fs_tutorial.csh-rwxr-xr-x 1 root wheel 25884 May 14 17:17 test_recon-all.csh-rwxr-xr-x 1 root wheel 668968 May 14 17:17 tetgen-rwxr-xr-x 1 root wheel 3231 May 14 17:17 thickdiffmap-rwxr-xr-x 1 root wheel 102 May 14 17:17 tkmedit-rwxr-xr-x 1 root wheel 8859 May 14 17:17 tkmeditfv-rwxr-xr-x 1 root wheel 106 May 14 17:17 tkregister2-rwxr-xr-x 1 root wheel 6493700 May 14 17:17 tkregister2_cmdl-rwxr-xr-x 1 root wheel 103 May 14 17:17 tksurfer-rwxr-xr-x 1 root wheel 43553 May 14 17:17 trac-all-rwxr-xr-x 1 root wheel 26633 May 14 17:17 trac-paths-rwxr-xr-x 1 root wheel 58360 May 14 17:17 trac-preproc-rwxr-xr-x 1 root wheel 15106 May 14 17:17 tractstats2table-rwxr-xr-x 1 root wheel 75180 May 14 17:17 tridec-rwxr-xr-x 1 root wheel 110675 May 14 17:17 unpack_ima.tcl-rwxr-xr-x 1 root wheel 45265 May 14 17:17 unpack_ima1.tcl-rwxr-xr-x 1 root wheel 38901 May 14 17:17 unpack_mnc.tcl-rwxr-xr-x 1 root wheel 6596 May 14 17:17 unpackimadir-rwxr-xr-x 1 root wheel 35562 May 14 17:17 unpackimadir2-rwxr-xr-x 1 root wheel 18546 May 14 17:17 unpackmincdir-rwxr-xr-x 1 root wheel 145 May 14 17:17 unpacksdcmdir-rwxr-xr-x 1 root wheel 46836 May 14 17:17 unpacksdcmdir.tcl-rwxr-xr-x 1 root wheel 4690 May 14 17:17 usbtree-rwxr-xr-x 1 root wheel 3743 May 14 17:17 vno_match_check-rwxr-xr-x 1 root wheel 7108540 May 14 17:18 volume_copy_test_cuda-rwxr-xr-x 1 root wheel 4659 May 14 17:18 vsm-smooth-rwxr-xr-x 1 root wheel 3339 May 14 17:18 vtk_setup-rwxr-xr-x 1 root wheel 5376 May 14 17:18 wfilemask-rwxr-xr-x 1 root wheel 7046 May 14 17:18 wm-anat-snr-rwxr-xr-x 1 root wheel 2550 May 14 17:18 xfmrot-rwxr-xr-x 1 root wheel 9128 May 14 17:18 xhemireg-rwxr-xr-x 1 root wheel 445416 May 14 17:18 xmlToHtml-rwxr-xr-x 1 root wheel 5265 May 14 17:18 xsanatreg-rwxr-xr-x 1 root wheel 23032 May 14 17:18 zero_lt_4dfp ----Messaggio originale---- Da: zkaufman(a)nmr.mgh.harvard.edu Data: 7-giu-2013 18.02 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] mris resample: Command not found. This error is permanent after new patch download Stefano, step 4 should be: "chmod +x $FREESURFER_HOME/bin/mris_resample" When you do an "ls -l" in the $FREESURFER_HOME/bin directory, you need to see the to see the x's next to mris_resample just like you do with all the other files in that directory. -Zeke On 06/07/2013 11:49 AM, stdp82(a)virgilio.it wrote: > Hi list, > > during trac-all -prep I have this error: > > MRISregister() return, current seed 0 > writing registered surface to > /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg... > expanding nbhd size to 1 > mris_resample: Command not found. > Darwin iMac > > I have performed my analysis by the following steps (as recommended by > Zeke and Lilla): > > 1. download "unKnow" file (7.6 MB) at > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample > 2. put file in $FREESURFER/bin/ > 4. chmod +x ~/mris_resample as recommended by Daniel (in the first test > I did not use this command) > 5. start trac-all -prep > 6. ERROR (in inter-reg step) > > What's happen? > > Thank you very much, > > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

1 0

mris resample: Command not found. This error is permanent after new patch download
by stdp82＠virgilio.it 07 Jun '13

07 Jun '13

Hi list, during trac-all -prep I have this error: MRISregister() return, current seed 0writing registered surface to /Applications/freesurfer/subjects/subject_prova/Diff03/surf/rh.cvs.tocvs_avg35.sphere.reg...expanding nbhd size to 1mris_resample: Command not found.Darwin iMac I have performed my analysis by the following steps (as recommended by Zeke and Lilla): 1. download "unKnow" file (7.6 MB) at ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/mris_resample2. put file in $FREESURFER/bin/4. chmod +x ~/mris_resample as recommended by Daniel (in the first test I did not use this command)5. start trac-all -prep6. ERROR (in inter-reg step) What's happen? Thank you very much, Stefano

3 2

Yeo_JNeurophysiol11_FreeSurfer.zip
by Peter Savadjiev 07 Jun '13

07 Jun '13

Hello, I'm trying to download ftp://surfer.nmr.mgh.harvard.edu/pub/data/Yeo_JNeurophysiol11_FreeSurfer.zip (as linked from http://www.freesurfer.net/fswiki/CorticalParcellation_Yeo2011) however, the file doesn't seem to be available, or the server is not responsive. Is there another location from where I could download this file? Thank you, Peter

3 2

mris_preproc --qdec-long problem
by Martin Reuter 07 Jun '13

07 Jun '13

Hi Chris, this is a good question for the list (cc'ed), others may or will have the same problem. The problem is with your table file, specifically the new line character. DOS uses \r\n , Mac \r and Linux \n. Your text file uses \r, so it probably was created on a mac. The problem is that the "cat" command (at least in linux) does not work on your file: cat long.qdec.table.dat is empty You can convert the \r to \n (linux format): tr '\r' '\n' < long.qdec.table.dat > long2.qdec.table.dat and then should be able to run the preproc command. People with DOS formats should not run the above "tr' command as they will end up with 2 newlines instead of 1. Maybe DOS txt files work with 'cat' directly (so there is no need)? If anyone on the list knows a good way of cat and awk a file independently of the new line (and working on all OS), let me know. This is the command I use: cat $fsgdf | awk '{if ($1 != "fsid" && substr($1,0,1) != "#") printf("%s.long.%s\n", $1, $2)}' to generate the subjects id's from the table's first two columns. Best, Martin On 06/03/2013 03:45 PM, Christopher McCarthy wrote: > Dr. Reuter, > > We corresponded in the past about QDEC, and you gave me great help. > The lab I work for is now moving towards using the Longitudinal Mixed > Effects Model. When I go to run the command: > > mris_preproc --qdec-long ./qdec/long.qdec.table.dat --target > study_average --hemi lh --meas thickness --out lh.thickness.mgh > > I get the error: 'ERROR: no subjects specified.' I am attaching my > long.qdec.table.dat, which works fine when loaded by QDEC. Do you > have any idea of why I am getting this error? > > Thanks, > > Chris McCarthy -- Martin Reuter, Ph.D. Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreuter(a)nmr.mgh.harvard.edu reuter(a)mit.edu Web : http://reuter.mit.edu

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Control points: possible bug (only tested in 5.3)
by Garikoitz Lerma-Usabiaga 07 Jun '13

07 Jun '13

Hi list, I've been creating control points and I got the following error: MRIwriteControlPoints(/home/glerma/freesurfer/subjects/TNT/TNT_solosubs/S_11/tmp/control.dat): could not open file No such file or directory I created the /tmp/ folder by hand and then it created the control.dat file properly (going to tkmedit > File > Save Control Points). These are the permission on the S_11 folder: drwxrwxr-x 17 glerma domain users 4096 Jun 7 09:41 S_11 (this is a CentOS 5 machine) thanks! Gari

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