Freesurfer January 2016

freesurfer@nmr.mgh.harvard.edu

130 participants
204 discussions

Crashing with Fedora 23
by Barron, Daniel 28 Jan '16

28 Jan '16

Hi List, We just upgraded our Linux Box to Fedora 23 and installed csh so recon-all would run, yet we’re still getting crashed analyses. Here is the error from my recon-all.error file: ------------------------------ SUBJECT 2_03T_N12_12_18441 DATE Thu Jan 21 16:20:16 GMT 2016 USER dsbarron HOST psyws26.psych.ox.ac.uk PROCESSOR x86_64 OS Linux Linux psyws26.psych.ox.ac.uk 4.3.3-300.fc23.x86_64 #1 SMP Tue Jan 5 23:31:01 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.73 2013/05/12 23:15:37 nicks Exp $ /home/freesurfer/bin/recon-all PWD /home/dsbarron/Schmidt/Freesurfer/2_03T_N12_12_18441/mri CMD mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz Here is the error when I try to call just the mrinucorrect.mni function: bash-4.3$ mri_nu_correct.mni mri_nu_correct.mni:1: parser error : Start tag expected, '<' not found #! /bin/tcsh -f ^ Document not parsed successfully. Any suggestions/ideas? Please help! Thanks! Cheers, Daniel

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freeview: locate subcortical structures based on index
by Mihaela Stefan 28 Jan '16

28 Jan '16

Hello Freesurfers, I have a couple of questions (see also attachment): 1) How can I locate a subcortical structure in freeview using the Lookup Table? In Tracula, I click on a tract and it is highlighted on the brain. Is there a similar function of visualizing the aseg labels (for example, I want to highlight 18 Left-Amygdala)? 2) In the cursor and mouse information display, why, when I go through the slices on "aseg" in Y direction, the RAS changes in Z direction? Thanks! Mihaela

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Fwd: hardware question
by Joost Janssen 28 Jan '16

28 Jan '16

Hi, We're thinking of buying a computer with the main goal simultaneous processing of 'recon-all's'. the computer cannot be a 'cluster' and must be linux. These specs looked good to us: - Intel Core i7-5820K 3.3Ghz - Asus X99-A - Arctic Cooling Freezer A30 CPU Cooler - G.Skill Aegis DDR4 2400 PC4-19200 16GB CL15 - Samsung 850 Evo SSD Series 500GB SATA3 - Toshiba 4TB 7200rpm SATA3 - Aerocool Aero 800 Negra USB 3.0 - AeroCool KCAS 700W 80 Plus Bronze - Asus GeForce Strix GTX 960 DirectCU II OC 4GB GDDR5 Are there things we can improve at? Thanks for any advice! -joost

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Slice order default
by Rodriguez-Thompson, Anais 28 Jan '16

28 Jan '16

Hi Freesurfer experts, I just starting using slice time correction with a given slice order during pre-processing: preproc-sess -s GDDA001 -surface fsaverage lhrh -mni305 -so siemens -fwhm 5 -per-run Previously I had been using the same command, but without the -so designation. Out of curiosity, without that flag was it running slice time correction by default? And if it was, what slice order was it using by default? Thanks, Anais

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Re: [Freesurfer] recon-all: core dumped error
by Fengji Geng 28 Jan '16

28 Jan '16

Hi Bruce, Below is our hardware/software information. Also curious, will install the newest development version of fs 6.0 solve our problem either? Thanks a lot! Linux 2.6.32-573.12.1.el6.x86_64 LSB Version: :base-4.0-amd64:base-4.0-ia32:base-4.0-noarch:core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch Distributor ID: RedHatEnterpriseServer Description: Red Hat Enterprise Linux Server release 6.7 (Santiago) Release: 6.7 Codename: Santiago freesurfer-Linux-centos6_x86_64-dev-20151215 ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Hi Fengji, it's called mris_ca_label, and yes, that is what I mean. If you tell us your hardware/software environment Zeke can get you a binary On Thu, 28 Jan 2016, Fengji Geng wrote: > > Hi Bruce, > > Did you mean an updated version of mri_parcellate? If so, it would be great. > > Thanks! > > ? > > -------------------------------------------- > > ? > > ? > > Hi Fengji > > ? > > this is a known bug in mris_parcellate. We can give you an updated > version > > if you want, but you should probably rerun all your subjects using it. > The > > good news is that it's fast - just a couple of min/hemi > > ? > > cheers > > Bruce > > ? On Tue, 26 Jan > > 2016, Fengji Geng wrote: > > ? > > > Hello fs experts, > > > > > > We ran a command like ?recon-all -all -s HMN002 > -hippocampal-subfields-T1T2 > > > HMN002/T2/*.mgz T1T2?. Then, there was an error as ?Abort (core dumped)? > > > (which is also attached below). The error log file is also attached here.? > > > > > > Error msg: > > >--------------------------------------------------------------------- > >------ > > > -------------------------- > > > setting seed for random number generator to 1234 > > > using ../mri/aseg.presurf.mgz aseg volume to correct midline > > > $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ > > > ? $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ > > > reading > > atlasfrom/cell_root/software/freesurfer/dev/sys/average/lh.curvature > > .buckner40.f > ille > > > d.desikan_killiany.2010-03-25.gcs... > > > reading color table from GCSA file.... > > > average std = 1.0?? using min determinant for regularization = 0.011 > > > 0 singular and 384 ill-conditioned covariance matrices regularized > > > input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature > > > labeling surface... > > > 1592 labels changed using aseg > > > relabeling using gibbs priors... > > > 000:?? 2975 changed, 134786 examined... > > > 001:??? 698 changed, 12707 examined... > > > 002:??? 152 changed, 3873 examined... > > > 003:???? 50 changed, 880 examined... > > > 004:???? 29 changed, 284 examined... > > > 005:???? 16 changed, 164 examined... > > > 006:????? 7 changed, 87 examined... > > > 007:????? 1 changed, 42 examined... > > > 008:????? 0 changed, 4 examined... > > > 206 labels changed using aseg > > > 000: 105 total segments, 64 labels (264 vertices) changed > > > 001: 43 total segments, 4 labels (14 vertices) changed > > > 002: 39 total segments, 0 labels (0 vertices) changed > > > 1 filter iterations complete (10 requested, 0 changed) > > > Abort (core dumped) > > > Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov > > 23 > > > 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux > > > > > > recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST > > 2016 > > > > > > Our freesurfer information: > > > -------- freesurfer-Linux-centos6_x86_64-dev-20151215 -------- > > > Setting up environment for FreeSurfer/FS-FAST (and FSL) > > > FREESURFER_HOME?? /cell_root/software/freesurfer/dev/sys > > > FSFAST_HOME?????? /cell_root/software/freesurfer/dev/sys/fsfast > > > FSF_OUTPUT_FORMAT nii.gz > > > SUBJECTS_DIR????? /export/data/hippocampus/HMN/data > > > MNI_DIR?????????? /cell_root/software/freesurfer/dev/sys/mni > > > FSL_DIR?????????? /cell_root/software/fsl/new/sys > > > > > > Looking forward to hearing how we can resolve this error. Also, > > thanks in > > > advance. > > > > > > Best, > > > > > > ----- Fengji > > > > > > > > >? > > ? > > ? > > --- > > Fengji > > ? > > > --- Fengji

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FreeSurfer 6 Release Date & El Capitan SIP issues
by Shady El Damaty 28 Jan '16

28 Jan '16

Hi, I was curious to know what the tentative release date for FreeSurfer 6 is. I’m currently running FreeSurfer on multiple machines with El Capitan installed and I’m wondering whether it’s worth installing the beta distribution or rather uninstalling SIP on each of these many machines. Also is there any documentation on any specific bugs to watch out for with El Capitan and FreeSurfer 5.3? I’ve been running some functions and haven’t found any errors yet. Thank you, Shady El Damaty PS - how does FreeSurfer 6 plan to get around SIP?

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mris_preproc on zipped data
by Lars M. Rimol 28 Jan '16

28 Jan '16

Hi, I have a large amount of data (FS scanworkups) where all the files within every subject's directory are zipped. Is there a way to run mris_preproc on zipped data? For instance, mris_preproc crashes because it can't find lh.thickness unless I unzip it Thank you! sincerely yours, Lars M. Rimol, PhD Senior researcher, Norwegian Advisory Unit for functional MRI Department of Radiology, St. Olav's University hospital, 7006 Trondheim, Norway

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Segmentation depends on image file format
by Parzer, Peter 28 Jan '16

28 Jan '16

Hi, we have brain images stored as DICOM and as NIFTI files. For some time we used to import the NIFTI files to freesurfer for segmentation. I was curious if it makes a difference if we would import the DICOM files directly, and was surprised that it actually did. Here are the commands we used: # Import DICOM files recon-all -s 3003PC_dcm -i ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm # Convert DICOM to NIFTI and import NIFTI file mri_convert ../../Daten/DICOM/3003PC/M_MPRAGE_sag/IM-0010-0001.dcm 3003PC.nii.gz recon-all -s 3003PC_nii -i 3003PC.nii.gz # Segmentation of DICOM file import recon-all -s 3003PC_dcm -all # Segmentation of NIFTI file import recon-all -s 3003PC_nii -all Here are the first 3 volumes from aseg.stats for 3003PC_dcm (DICOM import) 1 4 5612 5611.8 Left-Lateral-Ventricle 27.6355 12.8465 8.0000 93.0000 85.0000 2 5 452 452.2 Left-Inf-Lat-Vent 42.1100 14.9377 7.0000 86.0000 79.0000 3 7 13765 13765.1 Left-Cerebellum-White-Matter 87.7808 6.6008 36.0000 109.0000 73.0000 and here the the first 3 volumes for 3003PC_nii (NIFTI import) 1 4 5582 5582.2 Left-Lateral-Ventricle 27.4507 12.7212 8.0000 93.0000 85.0000 2 5 421 421.1 Left-Inf-Lat-Vent 40.8032 14.6554 7.0000 83.0000 76.0000 3 7 13899 13898.6 Left-Cerebellum-White-Matter 87.6707 6.7539 36.0000 109.0000 73.0000 The differences are small but I think there should be no differences at all. Has someone an explanation for this differences and which file format is better? Greetings Peter P. S.: Our system: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on Ubuntu 14.04

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Re mri_binarize --i sig.cluster.mgh --min 1.3 --o thresholded.mgh 1.3 = -log10(.05 {Disarmed}
by Erik Lindberg 28 Jan '16

28 Jan '16

Dear Bruce and Freesufers, I get the following message: surfer: Interpreting overlay volume /media/EHD/ALLA_FREESUFER_PROCESSING_TIDIS_NOMAS_AD/qdec/lh.kvot_gender.glmdir/Gend/thresholded.mgh as encoded scalar volume. the two volumes I tried to convert: 1) Volume information for sig.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 2) Volume information for cache.th13.abs.sig.cluster.mgh type: MGH dimensions: 163842 x 1 x 1 voxel sizes: 1.0000, 1.0000, 1.0000 type: FLOAT (3) fov: 163842.000 dof: 0 xstart: -81921.0, xend: 81921.0 ystart: -0.5, yend: 0.5 zstart: -0.5, zend: 0.5 TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees nframes: 1 PhEncDir: UNKNOWN ras xform present xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = 0.0000 : x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a = 0.0000 : x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s = 0.0000 talairach xfm : Orientation : LIA Primary Slice Direction: coronal voxel to ras transform: -1.0000 0.0000 0.0000 81921.0000 0.0000 0.0000 1.0000 -0.5000 0.0000 -1.0000 0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 voxel-to-ras determinant -1 ras to voxel transform: -1.0000 0.0000 0.0000 81921.0000 -0.0000 -0.0000 -1.0000 0.5000 -0.0000 1.0000 -0.0000 0.5000 0.0000 0.0000 0.0000 1.0000 Although both these overlays have significant areas - nothing appears on the binarized version after the conversion Best wishes, Olof Lindberg Olof Lindberg PhD Novum plan 5 NVS department section clinical geriatrics 14186 Stockholm +46722255711 http://www.oloflindberg.se <https://email.ki.se/owa/redir.aspx?SURL=J0wY4rfFaJiRdznonoXdg3ld1xD2HSpgTJI…>

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Re: [Freesurfer] recon-all: core dumped error (Bruce Fischl)
by Fengji Geng 28 Jan '16

28 Jan '16

Hi Bruce, Did you mean an updated version of mri_parcellate? If so, it would be great. Thanks! -------------------------------------------- Hi Fengji this is a known bug in mris_parcellate. We can give you an updated version if you want, but you should probably rerun all your subjects using it. The good news is that it's fast - just a couple of min/hemi cheers Bruce On Tue, 26 Jan 2016, Fengji Geng wrote: > Hello fs experts, > > We ran a command like ?recon-all -all -s HMN002 -hippocampal-subfields-T1T2 > HMN002/T2/*.mgz T1T2?. Then, there was an error as ?Abort (core dumped)? > (which is also attached below). The error log file is also attached here.? > > Error msg: > --------------------------------------------------------------------------- > -------------------------- > setting seed for random number generator to 1234 > using ../mri/aseg.presurf.mgz aseg volume to correct midline > $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ > ? $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $ > reading atlas from/cell_root/software/freesurfer/dev/sys/average/lh.curvature.buckner40.fille > d.desikan_killiany.2010-03-25.gcs... > reading color table from GCSA file.... > average std = 1.0?? using min determinant for regularization = 0.011 > 0 singular and 384 ill-conditioned covariance matrices regularized > input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature > labeling surface... > 1592 labels changed using aseg > relabeling using gibbs priors... > 000:?? 2975 changed, 134786 examined... > 001:??? 698 changed, 12707 examined... > 002:??? 152 changed, 3873 examined... > 003:???? 50 changed, 880 examined... > 004:???? 29 changed, 284 examined... > 005:???? 16 changed, 164 examined... > 006:????? 7 changed, 87 examined... > 007:????? 1 changed, 42 examined... > 008:????? 0 changed, 4 examined... > 206 labels changed using aseg > 000: 105 total segments, 64 labels (264 vertices) changed > 001: 43 total segments, 4 labels (14 vertices) changed > 002: 39 total segments, 0 labels (0 vertices) changed > 1 filter iterations complete (10 requested, 0 changed) > Abort (core dumped) > Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov 23 > 12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST 2016 > > Our freesurfer information: > -------- freesurfer-Linux-centos6_x86_64-dev-20151215 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME?? /cell_root/software/freesurfer/dev/sys > FSFAST_HOME?????? /cell_root/software/freesurfer/dev/sys/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR????? /export/data/hippocampus/HMN/data > MNI_DIR?????????? /cell_root/software/freesurfer/dev/sys/mni > FSL_DIR?????????? /cell_root/software/fsl/new/sys > > Looking forward to hearing how we can resolve this error. Also, thanks in > advance. > > Best, > > ----- Fengji > > > --- Fengji

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Freesurfer January 2016