Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

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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if: Expression Syntax.
by Lars M. Rimol 28 Jan '16

28 Jan '16

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Re: [Freesurfer] mritotal failed - help with manual registration (Bruce Fischl)
by will brown 28 Jan '16

28 Jan '16

Hi Bruce, I've attached a shot of the misalignment as seen in freeview. Yes the original images were DICOM created in Siemens machine T1, 0.8 slice thickness, can provide all DICOM tags if needed. Thanks, Will On Tue, Jan 26, 2016 at 6:00 AM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > 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: mritotal failed - help with manual registration (Bruce Fischl) > 2. recon -all errors (Jasmin Alves) > 3. Re: Processing .mnc files (Ankita Chatterjee) > 4. Re: Processing .mnc files (Bruce Fischl) > 5. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) > 6. hippocampal subfields - multispectral segmentation with FLAIR > (Luigi Antelmi) > 7. Re: hippocampal subfields - multispectral segmentation with > FLAIR (Eugenio Iglesias) > 8. Re: recon -all errors (Bruce Fischl) > 9. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) > 10. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Erik Lindberg) > 11. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Bruce Fischl) > 12. FDR map: hide very little cluster (stdp82(a)virgilio.it) > 13. [All] position available immediately (Bruce Fischl) > 14. Re: mri_binarize --i sig.cluster.mgh --min 1.3 --o > thresholded.mgh 1.3 = -log10(.05) (Douglas Greve) > 15. Re: FDR map: hide very little cluster (Douglas Greve) > 16. R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) > 17. R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) > 18. Re: R: Re: FDR map: hide very little cluster (Douglas N Greve) > 19. R: R: Re: FDR map: hide very little cluster (stdp82(a)virgilio.it) > 20. Re: R: R: Re: FDR map: hide very little cluster (Douglas N Greve) > 21. R: Re: R: Re: FDR map: hide very little cluster > (stdp82(a)virgilio.it) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 24 Jan 2016 18:58:54 -0500 (EST) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mritotal failed - help with manual > registration > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <alpine.LRH.2.20.1601241858240.29174(a)door.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII; format=flowed > > Hi Will > > can you take the same images with freeview and send them along? Also: > tell us a bit about your images. What format did they start in? Were they > dicoms? > > Bruce > > On Mon, 25 Jan 2016, will brown wrote: > > > Hi all, > > After attempting recon-all I received the error "mritotal failed, see > > transforms/talairach.log" etc which I understand may have something to do > > with bad output from registration. I've checked orig.mgz which does look > out > > of line - the orientation is off so that it appears the subject has their > > head tilted off to one side (see Image1.jpg). > > > > I have tried to fix this manually with the help of this tutorial: > > > > http://freesurfer.net/fswiki/FsTutorial/Talairach_freeview > > > > Hovever, the "movable" blurry image that I'm trying to line up with my > > subjects image does not match the coronal, sagittal or horizontal views, > > e.g. when I click "coronal" my subject is displayed correctly but the > > movable image is displayed horizontally (see Image2.jpg and Image3.jpg). > > > > Am I missing something obvious? (and am I even on the right track given > this > > error?) > > > > Thanks in advance for any help. > > > > Cheers, > > Will > > > > > > > ------------------------------ > > Message: 2 > Date: Sun, 24 Jan 2016 18:36:11 -0800 > From: Jasmin Alves <jalves(a)usc.edu> > Subject: [Freesurfer] recon -all errors > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > Message-ID: > <CACuamQ5whG9jjQLPvD5Hq4BAF+=C4ZvrACb3PrF2+KAx=aLN= > Q(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello Freesurfer, > > I am trying to learn freesurfer and ran into the following issues below > running the recon -all command. > > FREESURFER_HOME: /Applications/freesurfer > > Build stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > Kernel info: Darwin 14.5.0 x86_64 > > 1) > > joya > > 2) > > Jasmins-MacBook-Pro:subjects jasminalves$ recon-all -i > T1_original_joya.nii -subject joya -all & > > > 3) > > [1] 12300 > > Jasmins-MacBook-Pro:subjects jasminalves$ mkdir: > /Applications/freesurfer/subjects/joya: Permission denied > > mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied > > mkdir: /Applications/freesurfer/subjects/joya/scripts: Permission denied > > cp: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No such > file or directory > > cat: /Applications/freesurfer/subjects/joya/scripts/build-stamp.txt: No > such file or directory > > INFO: FreeSurfer build stamps do not match > > Subject Stamp: > > Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 > > INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects > > Actual FREESURFER_HOME /Applications/freesurfer > > /Applications/freesurfer/subjects/joya: No such file or directory. > > > [1]+ Exit 1 recon-all -i T1_original_joya.nii -subject > joya -a > Thank you, > Jasmin > > Jasmin Alves > Predoctoral Student > Medical Biology Graduate Program > University of Southern California > jalves(a)usc.edu >

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wm correction
by maryam koochaki 28 Jan '16

28 Jan '16

Hi Bruce, I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral Ventricle. As you can see in the image attached, the big part is excluded in both hemisphere. I tried to fill it by editing wm volume but the problem still exists.Do you have any suggestion?Thanks,Maryam test_vumc_158_rh.png test_vumc_158_lh.png

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