Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30133 discussions

Neuroimaging postdoctoral position
by Tiril Pedersen Gurholt 18 Jan '17

18 Jan '17

Dear All, At the NORMENT – K.G. Jebsen Research Centre for Psychosis Research, a Centre of Excellence, Institute of Clinical Medicine, University of Oslo, there is a position available as a postdoctoral student funded by the Research Council of Norway. The research area is psychiatric neuroimaging with focus on analysis of structural and functional, DTI and ASL MR imaging datasets with regard to developmental trajectories and genetic, environmental and phenotypic variation. Applicants should have a doctoral degree (PhD) in neuroimaging, computer science, bioinformatics, psychiatry, psychology or equivalent. Applicants who have handed in their dissertation for evaluation are also encouraged to apply, caveat the dissertation is approved. The application deadline is January 25, 2017. For further information and to submit an application please also see http://uio.easycruit.com/vacancy/1719677/70331?iso=no . Best regards, Tiril Gurholt --- Tiril Gurholt Postdoctoral Fellow Psychosis Research Centre, NORMENT Institute of Clinical Medicine, University of Oslo, Norway http://www.med.uio.no/norment/ [cid:image001.png@01D21DA0.544E82D0]

1 0

recon-all error (Freesurfer)
by Gwang-Won Kim 18 Jan '17

18 Jan '17

1 0

FS Anatomic ROIs Atlas
by Da, Xiao 17 Jan '17

17 Jan '17

Dear Freesurfer Community, I am wondering if you have these anatomic ROIs (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation) already done for the 3D volumetric standard MNI brain (either ch2 single subject brain(preferred) or 152 average brain) Greatly appreciated it. Thanks and best regards, Xiao Da Biomedical Engineer - Programmer Analyst II Functional Neuroimaging Laboratory Brigham and Women's Hospital 221 Longwood Avenue, Braunwald Building, Room LM116 Boston, MA 02115 xda(a)bwh.harvard.edu<mailto:xda@bwh.harvard.edu>

2 1

Anatomical ROI parcellation
by Aya Kabbara 17 Jan '17

17 Jan '17

Dear Freesurfer team, I am wondering is there a way using tksurfer to edit a given atlas (for example: destrieux atlas). I would like to parcellate the superior temporal region into three regions . Is there a way to do that? Thank you Aya

2 1

Re: [Freesurfer] V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream
by Antonin Skoch 17 Jan '17

17 Jan '17

Dear Martin, thank you for the feedback. I read the wiki but the instructions concerning aseg edits were not much clear for me. And, I was misinformed by -noasegfusion option. The pity with aseg errors is that with the current design and when the error is large to affect surfaces in base, it is necessary to edit the same error twice. Since the aseg of base is not initialized from cross, and long is not initialized from base, then one has to edit the same error both in base and in long (or cross). If there is a systematic error which affects all timepoints (as it is in my case - I have 2 points), I effectively have to edit the same error 3 times. It is quite large error affecting whole posterior part of lateral ventricle (see screenshot). Therefore, I thought that best option would be to edit the base and initialize long from base using -noasegfusion. I tried to do that by manually copying aseg from base and manually running mri_ca_label with -r and -ri option (and and the error is (almost) cleaned in long. Why do you think that the initialization from base is worse/undesirable than initialization from fused aseg from cross? It seems to me that to initialize from fused (averaged) asegs of cross or initialize from aseg of base (which is averaged template of cross) is methodologically quite similar, should produce similar results and in terms of edits it is much more convenient way. Regards, Antonin Hi Antonin, the -noasegfusion is not really supported and a left over from initial testing when we first developed the stream. I will take a look at it and probably remove the flag (or implement it in a way that it really initializes with the aseg from the base, although I think this is not desirable, unless one really assumes there is no/ or very little change between time points. About aseg edits in longitudinal processing, please look at our edit wiki page: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz <https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits#aseg.mgz> “ ASEG edits can be done in cross, base and long. Recommendation: Edit in long only if you want to correct the volume of important structures. Edit in base if surfaces need to be changed due to incorrect labeling of aseg. Not necessary to edit in cross. The segmentation in the long runs is initialized with a fused aseg (a weighted average of the cross sectional asegs). Thus any edits done to the cross sectionals are incorporated indirectly into the long stream. But since the fused aseg is used only for the initialization, it can happen that manual edits from the cross get removed again. Therefore, to correct the volume, just edit the long." So for your ventricle correction, you could either clean up the cross data and hope it caries over to the long (it should), or directly edit the long aseg. Best, Martin > On 16 Jan 2017, at 23:23, Antonin Skoch <a...(a)ikem.cz> wrote: > > Dear experts, > > I am testing the longitudinal stream with V6beta version. > > The recon-all -help says for -noasegfusion: > > Do not create 'fused' aseg from the longbase timepoints, which would normally > be used to initialize the ca_labeling. Instead, initialize using the longbase > aseg.mgz. > > As I looked to recon-all code it seems that in case of -noasegfusion there is > no use of -r and -ri parameters and therefore no "initialization". Could you > please comment on? > > My second query is regarding manual edits: > > In one subject the manual editing of aseg was necessary due to ventricle > mislabeling. I edited the aseg.presurf in base template and subsequently run > longitudinal stream via > > recon-all -long tpID templateID -noasegfusion -all > > From the last sentence of -noasegfusion help I (wrongly) expected that my > aseg.presurf edits in base template would be incorporated for -long recon. > However, this was not the case, the edits have not been incorporated at all. > Looking at the recon-all code the aseg.presurf from base is never used for > -long. > > I thought that I could incorporate manual edits from base by manual copying > of aseg.presurf from base to long directory. As I looked for the way how the > manual aseg edits are handled in recon-all, they are identified by using the > difference between the files aseg.auto and aseg.manedit which contains manual > edits. Therefore I think that the copying from base is not an option, I > expect that this would replace segmentations not only in manual edit regions, > but in all regions where the aseg.auto of base and aseg.auto of -long differs > (they do not have the same input) which is undesirable. So I think I do not > have any other option than to edit aseg.presurf in -long again. > > Could you please comment on how to optimally handle such situations? > > Regards, > > Antonin Skoch > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

TRACULA in FreeSurfer 6.0 trac-paths error
by Derek A Pisner 17 Jan '17

17 Jan '17

Hi Anastasia, I am getting the following error when running trac-all –paths on all of my diffusion images using the newly updated TRACULA: *vlogin03.ls5(97)$* /work/04171/dpisner/stampede/Applications/freesurfer/bin/trac-all -no-isrunning -path -c /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/trac_config.txt niiRead(): NIFTI_UNITS_UNKNOWN, assuming mm WARNING: niiRead(): unknown time units 0 in /work/04171/dpisner/data/ABM/TRACULA/tractography_output/s002/dmri/dwi.nii.gz Any idea what’s going on here? Thanks as always, Derek Pisner Doctoral Student CLA 4.600 Mood Disorders Laboratory (MDL) Department of Psychology | The University of Texas at Austin P.S. Here is the header information on my dwi.nii.gz file: *vlogin03.ls5(105)$* fslhd dwi.nii.gz filename dwi.nii.gz sizeof_hdr 348 data_type FLOAT32 dim0 4 dim1 115 dim2 115 dim3 56 dim4 55 dim5 1 dim6 1 dim7 1 vox_units Unknown time_units Unknown datatype 16 nbyper 4 bitpix 32 pixdim0 0.000000 pixdim1 2.000000 pixdim2 2.000000 pixdim3 2.000000 pixdim4 1.000000 pixdim5 1.000000 pixdim6 1.000000 pixdim7 1.000000 vox_offset 352 cal_max 0.0000 cal_min 0.0000 scl_slope 1.000000 scl_inter 0.000000 phase_dim 0 freq_dim 0 slice_dim 0 slice_name Unknown slice_code 0 slice_start 0 slice_end 0 slice_duration 0.000000 time_offset 0.000000 intent Unknown intent_code 0 intent_name intent_p1 0.000000 intent_p2 0.000000 intent_p3 0.000000 qform_name Unknown qform_code 0 qto_xyz:1 2.000000 0.000000 0.000000 0.000000 qto_xyz:2 0.000000 2.000000 0.000000 0.000000 qto_xyz:3 0.000000 0.000000 2.000000 0.000000 qto_xyz:4 0.000000 0.000000 0.000000 1.000000 qform_xorient Left-to-Right qform_yorient Posterior-to-Anterior qform_zorient Inferior-to-Superior sform_name Aligned Anat sform_code 2 sto_xyz:1 -2.000000 0.000000 0.000000 114.551003 sto_xyz:2 0.000000 2.000000 0.000000 -74.456001 sto_xyz:3 0.000000 0.000000 2.000000 -0.960182 sto_xyz:4 0.000000 0.000000 0.000000 1.000000 sform_xorient Right-to-Left sform_yorient Posterior-to-Anterior sform_zorient Inferior-to-Superior file_type NIFTI-1+ file_code 1 descrip aux_file -- Derek Pisner

2 8

V6beta: recon-all --noasegfusion does not initialize using longbase aseg.mgz; how to handle aseg edits in longitudinal stream
by Antonin Skoch 17 Jan '17

17 Jan '17

Dear experts, I am testing the longitudinal stream with V6beta version. The recon-all -help says for -noasegfusion: Do not create 'fused' aseg from the longbase timepoints, which would normally be used to initialize the ca_labeling. Instead, initialize using the longbase aseg.mgz. As I looked to recon-all code it seems that in case of -noasegfusion there is no use of -r and -ri parameters and therefore no "initialization". Could you please comment on? My second query is regarding manual edits: In one subject the manual editing of aseg was necessary due to ventricle mislabeling. I edited the aseg.presurf in base template and subsequently run longitudinal stream via recon-all -long tpID templateID -noasegfusion -all >From the last sentence of -noasegfusion help I (wrongly) expected that my aseg.presurf edits in base template would be incorporated for -long recon. However, this was not the case, the edits have not been incorporated at all. Looking at the recon-all code the aseg.presurf from base is never used for -long. I thought that I could incorporate manual edits from base by manual copying of aseg.presurf from base to long directory. As I looked for the way how the manual aseg edits are handled in recon-all, they are identified by using the difference between the files aseg.auto and aseg.manedit which contains manual edits. Therefore I think that the copying from base is not an option, I expect that this would replace segmentations not only in manual edit regions, but in all regions where the aseg.auto of base and aseg.auto of -long differs (they do not have the same input) which is undesirable. So I think I do not have any other option than to edit aseg.presurf in -long again. Could you please comment on how to optimally handle such situations? Regards, Antonin Skoch

2 1

T2 voxel size needed for recon_all
by Erik O'Hanlon 17 Jan '17

17 Jan '17

2 2

Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream
by Tamara Tavares 16 Jan '17

16 Jan '17

Hi Dr. Reuter. Thank you again for your help. I ran the following command: "mri_robust_register --mov rawavg_1.mgz --dst rawavg_2.mgz --lta v1to2.lta --affine --satit" on the two rawavg.mgz images; one from each time point from the cross-sectional outputs. I have attached the information from the terminal and the output. Are these outputs appropriate to find the scaling information? If so, where can I find it? I am not very familiar with transformations, thus any information or directions to resources I can use would be very much appreciated. Thank you in advance for you help. Best, Tamara Message: 6 Date: Tue, 10 Jan 2017 21:18:34 +0100 From: Martin Reuter <mreuter(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Brighter image at baseline vs. follow up using longitudinal processing stream To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <9BCB373D-D368-4B36-B607-69E6A14AF952(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="us-ascii" Hi Tamara, mvoing in and popping out sounds like a scaling problem. We do only rigid transforms, so the scaling would already be in your original inputs. If that is the case, it could mean that there was a scanner calibration or something that caused scaled images and that would not be good. It should however appear in all images that have the calibration in between time points. You can try to use mri_robust_register with the affine flag to see if any scaling is present in the rawavg.mgz images between the two time points (it should report scaling separately on the screen output), else use lta_diff with the appropriate flags. You can also look at the affininely registered images and see if it looks better. Anyway if there is global scaling in the images, I would try to investigate a where this comes from and also drop that image from the study. Best, Martin

2 2

createMorph & applyMorph: unexpected results
by Stefano Zappalà 16 Jan '17

16 Jan '17

Hello FreeSurfer Developers, I'm attempting to apply the CVS output transformation "final_CVSmorph_toSynthF.m3z" to an image different to the one that was used for its estimation. I followed the steps reported at the bottom of the page https://surfer.nmr.mgh.harvard.edu/fswiki/mri_cvs_register, adjusting the lines for the output files that I obtained from mri_cvs_register. So I called for createMorph --out fullCVSmorph.tm3d --template MniNick.mgz --subject w_MniNick.mgz --in gcam final_CVSmorph_toSynthF.m3z morph el_reg_toSynthF.mgz and applyMorph --template MniNick.mgz --transform fullCVSmorph.tm3d vol w_MniNick.mgz outputvol.nii trilinear but I encountered the following output when running createMorph: setting orig areas to linear transform determinant scaled 1.00 atlas geometry = 256 , 256 , 256 image geometry = 256 , 256 , 256 vox 2 ras atlas = -1.00000 0.00000 0.00000 127.00000; 0.00000 0.00000 1.00000 -145.00000; 0.00000 -1.00000 0.00000 147.00000; 0.00000 0.00000 0.00000 1.00000; ras 2 vox image = -1.00000 -0.00000 -0.00000 90.00000; -0.00000 1.00000 -0.00000 126.00000; -0.00000 -0.00000 1.00000 72.00000; -0.00000 -0.00000 -0.00000 1.00000; product = 1.00000 0.00000 0.00000 -37.00000; 0.00000 0.00000 1.00000 -19.00000; 0.00000 -1.00000 0.00000 219.00000; 0.00000 0.00000 0.00000 1.00000; transform at origin -37.00000; -19.00000; 219.00000; 1.00000; invalid voxel count = 0 extension = mgz terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted (core dumped) I've searched the mailing list and no similar errors have been reported. The recon-all and mri_cvs_register calls seemed to have correctly terminated. Does anyone have any thoughts on how to trouble-shoot this one? 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-dev-20161130-24fa2c9 2) Platform: ubuntu 16.04 LTS 3) In the attachment: 3.1) log files of the mri_cvs_register execution; 3.2) log file of the recon-all executions on the moving and fixed images. Thank you for your consideration. Stefano.

2 2

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer