Freesurfer March 2018

freesurfer@nmr.mgh.harvard.edu

115 participants
161 discussions

mri_segment error
by Z Hessam 19 Mar '18

19 Mar '18

Hello FreeSurfer develpers I'm attempting to run " recon-all " command on a file of dicom data, and encounter with an error command: recon-all -s dyegmoh exited with ERRORS at Thu Feb 8 17:08:16 +0330 2018 how can i understand why this error happens and what should i do to solve it?

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mir_vol2surface registration file error
by Charlotte Grosse Wiesmann 19 Mar '18

19 Mar '18

Hi Shrishti, 1) by recon-all I meant recon-all in the freesurfer pipeline ( https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all ) to reconstruct the subject's cortical surfaces because if I got you right you have the maps on the surface (SN_like_cortical_lh.gz) and in the volume. If you only want to compare the maps in the volume you can skip this part I only compare the volume maps. 2) As far as I know with mri_vol2surf and tksurfer you can use a number of different formats including .nii (if not you can convert with mri_convert) 3) I'm not sure I understand your question. Make sure both of your volume maps are registered to the same MNI152 template. (Best is if you ask the people who gave you their maps to also give you the template. Then you can register your template to that template (e.g., using ANTS) and the transformation matrix you obtain to map your maps onto the other template.) If both volume maps are in the same space you can both open them with fslview on the template they have been registered to (fslview template.nii map1.nii map2.nii) and compare them visually. Best Charlotte ----- Original Message ----- From: "23srishtigoel" <23srishtigoel(a)gmail.com> To: "wiesmann" <wiesmann(a)cbs.mpg.de> Sent: Sunday, March 18, 2018 5:37:40 PM Subject: Re: [Freesurfer] mir_vol2surface registration file error Hi Charlotte, Thank you so much for your help, I really appreciate it and this is super helpful for me. I just want to clarify a couple small thing 1) By running recon-all on that subject do you mean reconstructing that subject's DICOM basically? 2) I notice that the extension you are using is .mgh so would I have to convert the volume maps (which is SN_like_cortical.nii) into mgh/mgz/gz as well? 3) Also, would you be able to elaborate a little on how to view the volumes on the MNI. I have used fslview and I think I know how to map our volume maps on the MNI152 volume space but I am not sure what would be the best way to use fslview to view it. Thanks once again! Best, Srishti Best, Srishti Social/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srishtig(a)email.unc.edu skype: srishti.goel12 On Sun, Mar 18, 2018 at 10:55 AM, Charlotte Grosse Wiesmann < wiesmann(a)cbs.mpg.de> wrote: > Hi Srishti, > > I had a similar problem recently, so I will try to help. To compare your > maps with the surface maps SN_like_cortical_lh.gz of the others you need to > map your volume to the surface of the same subject they are using. > > That is, you first have to run recon-all on that subject (unless they gave > you the link to the subject folder for which recon-all has already been > run. Say, the name of the subject folder is SUBJECT-ID). > > Then, you need to map your volume to the surface of that subject: > mri_vol2surf --src negative_allsocial_proportion.nii --regheader > SUBJECT-ID --hemi lh --o ./neg_allsocial_lh.mgh [more options] > > Then, you should be able to look at both surface maps on your subject > surface, e.g., with tksurfer > > tksurfer SUBJECT-ID lh inflated -overlay ./neg_allsocial_lh.mgh -overlay > SN_like_cortical_lh.mgh -fthresh 0.5 > > For the volume, you need to map your volume maps to the same MNI152 volume > space the other volume maps are in, and then you should be able to view > them both on the according MNI template with any brain volume viewer > program (e.g., fslview,...). > > Hope this helps. > > Best, > > Charlotte > > > > > ----- Original Message ----- > From: "srishti goel" <23srishtigoel(a)gmail.com> > To: "Freesurfer support list" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Saturday, March 17, 2018 2:48:23 PM > Subject: Re: [Freesurfer] mir_vol2surface registration file error > > Hi, > > I tried using bbregister to register my files with the following command: > > > bbregister --mov negative_allsocial.nii --bold --s SN_like_cortical_lh.gz > --init-rr --lta register.lta > > and this is the error I received: > > > reading source './tmp.bbregister.173331/template.nii'... > > mri_robust_register.bin: only pass single frame MRI source > ./tmp.bbregister.173331/template.nii. > > > > > No such file or directory > > > > > I would like to re-iterate my issue as that might be helpful. We have > carried out a meta analysis and want to compare our meta analytic maps to > someone's else's map. Our meta analytic map is negative_allsocial.vmp which > we converted to a nifti using neuroelf and now have the > negative_allsocial.nii. We want to see how someone else's map which is the > SN_like_cortical_lh.gz (they said to view this on a subject file to which > they gave us the link) compares to our map. We would also further want to > see how our map compares to their volume map which is > SN_like_subcortical.nii (these are in MNI152 volume space). We are using > mri_vol2surf to view compare the two files. > > > > > mri_vol2surf --src negative_allsocial_proportion.nii --src_type analyze > --srcreg [REGISTRATION MATRIX] --hemi lh --o ./neg_allsocial.nii --projfrac > 0.5 > > > > > > And for the registration matrix I tried using bbregister as told my the > freeSurfer help group. > > I can send the files as well if required and would highly appreciate some > prompt help on this. > > > > > Thanks so much! > > > > > Best, > > Srishti > > > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig(a)email.unc.edu > skype: srishti.goel12 > > > On Fri, Mar 9, 2018 at 11:15 AM, Douglas Greve < dgreve(a)mgh.harvard.edu > > wrote: > > > > > > You create it with bbregister. See the multimodal integration tutorial > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview > > On 3/6/18 6:36 PM, srishti goel wrote: > > > > I am sorry but that is what I am unsure about it. I don't know how to > obtain a registration matrix or which registration matrix to use for this. > > Best, > Srishti > Social/Clinical Research Specialist > Child Imaging Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srishtig(a)email.unc.edu > skype: srishti.goel12 > > > On Mon, Mar 5, 2018 at 3:24 PM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu > wrote: > > > Why did you remove the registration file? --srcreg below > > > On 02/28/2018 04:13 PM, srishti goel wrote: > > Hello, > > > > Thank you so much! I used the following command as you said and got an > > error : must specify a source registration file or --regheader > > > > mri_vol2surf --src negative_allsocial_avgnull.nii --src_type analyze > > --trgsubject fsaverage --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 > > > > > > Best, > > Srishti > > Social/Clinical Research Specialist > > Child Imaging Research and Life Experiences Lab > > University of North Carolina at Chapel Hill > > email (W): srishtig(a)email.unc.edu <mailto: srishtig(a)email.unc.edu > > > skype: srishti.goel12 > > > > > > On Wed, Feb 28, 2018 at 10:13 AM, Douglas Greve > > < greve(a)nmr.mgh.harvard.edu <mailto: greve(a)nmr.mgh.harvard.edu >> wrote: > > > > you need to add --trgsubject fsaverage to your mri_vol2surf > > command line > > > > > > On 2/27/18 12:23 PM, srishti goel wrote: > >> Hello, > >> > >> We are trying to project a volume map onto a surface. Our network > >> based volume map is a .vmp file and our surface is a nifti file. > >> We were able to convert the volume maps from .vmp to nifti. > >> Our volume map is: negative_allsocial_proportion.nii > >> Our surface is: SN_like_cortical_lh.nii > >> The output file is named: neg_allsocial.nii > >> > >> We are trying to use the following command to now project the > >> volume map on surface and the issues we are facing are: > >> 1) We are unsure of what the purpose of the registration file is > >> and where in the mir_vol2surf command should we specify the surface > >> 2) If it is a matrix for something related to the surface on > >> which we want to project our volume then how should we go about > >> obtaining the registration file appropriate for our comparison. > >> > >> _Command:_ > >> mri_vol2surf --src negative_allsocial_proportion.nii --src_type > >> analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o > >> ./neg_allsocial.nii --projfrac 0.5 > >> > >> _Then to project it:_ > >> tksurfer fsaverage lh inflated -ov neg_allsocail.nii > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> <mailto: Freesurfer(a)nmr.mgh.harvard.edu > > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> < https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto: Freesurfer(a)nmr.mgh.harvard.edu > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > < 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 > > < 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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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 > > > _______________________________________________ > 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 > > > 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. >

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mir_vol2surface registration file error
by srishti goel 18 Mar '18

18 Mar '18

Hello, We are trying to project a volume map onto a surface. Our network based volume map is a .vmp file and our surface is a nifti file. We were able to convert the volume maps from .vmp to nifti. Our volume map is: negative_allsocial_proportion.nii Our surface is: SN_like_cortical_lh.nii The output file is named: neg_allsocial.nii We are trying to use the following command to now project the volume map on surface and the issues we are facing are: 1) We are unsure of what the purpose of the registration file is and where in the mir_vol2surf command should we specify the surface 2) If it is a matrix for something related to the surface on which we want to project our volume then how should we go about obtaining the registration file appropriate for our comparison. *Command:* mri_vol2surf --src negative_allsocial_proportion.nii --src_type analyze --srcreg [REGISTRATION MATRIX] --hemi lh --o ./neg_allsocial.nii --projfrac 0.5 *Then to project it:* tksurfer fsaverage lh inflated -ov neg_allsocail.nii

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Freesurfer Input Imaging
by Daniel Alejandro Reyna Torres 16 Mar '18

16 Mar '18

Hello, is there any recommendation from Freesurfer for MRI images used during recon-all? i.e., should we use a sagittal MRI, coronal or transversal? For instance, I have one subject with these 3 different orientations. I ran recon-all on the 3 of them and got the results for the reconstruction. I was wondering how can we know which would be more accurate. I have a guess but not sure. Thanks team. Regards, Daniel

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complete list of structures for SubCortGray
by prasser 16 Mar '18

16 Mar '18

Hi, >From https://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats "SubCortGray - includes thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there). This is a simple voxel count of structures identified as subcortical GM." Could you please let me know if "thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there)" is the complete list of structures identified as subcortical GM or are there others? A simple voxel count of thalamus, caudate, hippocampus, amygdala, accumbens, ventral DC, substancia nigra (if there) does not seem to match the subcortgray value from aseg.stats. Versions 5.3, 6.0. Thanks.

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make_average_subject monkey data
by Francesca Strappini 16 Mar '18

16 Mar '18

Dear Experts, I'm trying to average two monkey brains. I run this command line: make_average_subject --subjects MonkeyCelia MonkeyCassis --out AVGmonkeys but it ended with errors. I run the recon-all for both monkyes with the option -notal-check because I had problems with the Talairach registration. I don't know if this could be the cause. Thanks a lot Francesca Tue Mar 13 20:04:06 CET 2018 /usr/local/freesurfer/subjects/AVGmonkeys /usr/local/freesurfer/bin/recon-all -s AVGmonkeys -cortribbon -aparc2aseg subjid AVGmonkeys setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize 8192 kbytes coredumpsize 0 kbytes memoryuse unlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 63682 maxlocks unlimited maxsignal 63682 maxmessage 819200 maxnice 0 maxrtprio 0 maxrttime unlimited total used free shared buff/cache available Mem: 16350220 4943572 7520800 278988 3885848 10739864 Swap: 19528700 0 19528700 ######################################## program versions used $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ $Id: mri_motion_correct.fsl,v 1.15 2016/02/16 17:17:20 zkaufman Exp $ mri_convert.bin -all-info ProgramName: mri_convert.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 FLIRT version 5.5 $Id: talairach_avi,v 1.13 2015/12/23 04:25:17 greve Exp $ mri_convert.bin --version stable6 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: tkregister2.c,v 1.132.2.1 2016/08/02 21:17:29 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 Program nu_correct, built from: Package MNI N3, version 1.12.0, compiled by nicks@terrier (x86_64-unknown-linux-gnu) on 2015-06-19 at 01:25:34 ProgramName: mri_make_uchar ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_make_uchar.c,v 1.4 2011/03/02 00:04:14 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize.c,v 1.88.2.3 2016/12/27 16:47:13 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_watershed.cpp,v 1.103 2016/06/17 18:00:49 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_gcut ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_gcut.cpp,v 1.14 2011/03/02 00:04:16 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segment.c,v 1.43.2.1 2016/10/27 22:24:52 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_label2label.bin ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_label2label.c,v 1.48.2.2 2016/12/12 14:15:26 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_em_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_em_register.c,v 1.105.2.1 2016/10/27 22:25:10 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_normalize ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_normalize.c,v 1.67.2.2 2016/10/27 22:25:09 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_register ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_register.c,v 1.96.2.3 2016/10/27 22:25:10 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_ca_label ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_ca_label.c,v 1.113.2.2 2016/10/27 22:25:10 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_pretess ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_pretess.c,v 1.22 2013/08/30 18:12:25 mreuter Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fill.c,v 1.119 2011/10/25 14:09:58 fischl Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_tessellate.c,v 1.38.2.1 2016/07/26 18:46:38 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_concatenate_lta.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_concatenate_lta.c,v 1.16 2015/11/21 00:06:20 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_normalize_tp2 ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_normalize_tp2.c,v 1.8 2011/03/02 00:04:23 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_smooth.c,v 1.30 2014/01/21 18:48:21 fischl Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_inflate.c,v 1.45 2016/01/20 23:42:15 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature.c,v 1.31 2011/03/02 00:04:30 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_sphere.c,v 1.61 2016/01/20 23:42:15 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_fix_topology.c,v 1.50.2.1 2016/10/27 22:25:58 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_topo_fixer ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_topo_fixer.cpp,v 1.29 2011/03/02 00:04:34 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_ca_label ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_euler_number ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_euler_number.c,v 1.10 2013/01/14 22:39:14 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_make_surfaces ProgramArguments: -all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_make_surfaces.c,v 1.164.2.4 2016/12/13 22:26:32 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_register ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_register.c,v 1.63 2016/01/20 23:43:04 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_volmask ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_volmask.cpp,v 1.26.2.2 2016/11/18 20:05:18 zkaufman Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_anatomical_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_anatomical_stats.c,v 1.79 2016/03/14 15:15:34 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mrisp_paint ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mrisp_paint.c,v 1.12 2016/03/22 14:47:57 fischl Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_curvature_stats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_curvature_stats.c,v 1.65 2015/06/04 20:50:51 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mris_calc ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mris_calc.c,v 1.54.2.1 2016/09/27 18:51:28 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ ProgramName: mri_robust_register.bin ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ ProgramName: mri_robust_template ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_and ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_and.c,v 1.4 2011/03/02 00:04:13 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_or ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_or.c,v 1.5 2013/03/20 15:03:29 lzollei Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_fuse_segmentations ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_fuse_segmentations.c,v 1.8 2011/03/02 00:04:15 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_segstats ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ProgramName: mri_relabel_hypointensities ProgramArguments: -all-info ProgramVersion: $Name: stable6 $ TimeStamp: 2018/03/13-19:04:06-GMT BuildTimeStamp: Jan 18 2017 16:38:58 CVS: $Id: mri_relabel_hypointensities.c,v 1.13 2015/05/15 18:44:10 nicks Exp $ User: francesca Machine: shalimpc Platform: Linux PlatformVersion: 4.4.0-116-generic CompilerName: GCC CompilerVersion: 40400 ####################################### GCADIR /usr/local/freesurfer/average GCA RB_all_2016-05-10.vc700.gca GCASkull RB_all_withskull_2016-05-10.vc700.gca AvgCurvTif folding.atlas.acfb40.noaparc.i12.2016-08-02.tif GCSDIR /usr/local/freesurfer/average GCS DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ####################################### #-------------------------------------------- #@# Cortical ribbon mask Tue Mar 13 20:04:06 CET 2018 /usr/local/freesurfer/subjects/AVGmonkeys/mri mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon AVGmonkeys SUBJECTS_DIR is /usr/local/freesurfer/subjects loading input data... computing distance to left white surface computing distance to left pial surface computing distance to right white surface computing distance to right pial surface hemi masks overlap voxels = 34535 writing volume /usr/local/freesurfer/subjects/AVGmonkeys/mri/ribbon.mgz ERROR: ribbon has non-zero value at location 0,0,0 Linux shalimpc 4.4.0-116-generic #140-Ubuntu SMP Mon Feb 12 21:23:04 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s AVGmonkeys exited with ERRORS at Tue Mar 13 20:26:58 CET 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

3 8

Mean baseline Cth for each subject in a cluster obtained from a spc analysis
by Fred Sampedro 16 Mar '18

16 Mar '18

Dear Freesurfer Experts, I ran a longitudinal Cth analysis and found a cluster with significant spc differences between two groups. It was easy to obtain the mean spc values in that cluster for all the subjects. However, I would also like to have a spreedsheet with the baseline mean Cth values in that cluster for all my subjects to correlate with other clinical measures. My attempt was: mri_segstats --i SPC_ANALYSIS_FOLDER/y.mgh --seg SPC_ANALYSIS_FOLDER/SUBANALYSIS/mc-z.abs.th13.sig.cluster.mgh --excludeid 0 --sum CTH_inSPC_cluster.sum But obviously this is not the correct way to obtain for each subject the mean Cth value in that cluster. Any help would be much appreciated! Thanks a lot in advance, Fred

2 1

Map mask from volume to surface for small volume correction in surface analyses (using my own template)
by Charlotte Grosse Wiesmann 16 Mar '18

16 Mar '18

Dear freesurfer experts, I would like to restrict my surface analyses (cortical thickness and surface area) to a mask from an fMRI meta-analysis using my own subject-specific template that I created with ANTS. So far, I have used Qdec and wanted to correct for cluster size running the Monte Carlo (MC) simulation on my own template. Now I would like to restrict the simulation to my mask to do a small volume correction in my regions of interest. I mapped the mask to my own template (in volume space) using ANTS (WarpImageMultiTransform) but how can I get this mask to the surface space to run the MC simulation on my own template within this mask? I was planning to do: mri_mcsim --o my_template/mult-comp-cor/my_template/lh/mymask --base mc-z --surface my_template ?h --nreps 10000 --mask mymask.mgz How do I get mymask.mgz in the correct space for this? And can I continue using Qdec or do I have to use glmfit for these analyses? In addition: is it also possible to do a small volume correction using FDR rather than cluster-size correction? Thanks for your help! Charlotte

3 6

Postdoctoral Fellow Position at the University of Pittsburgh
by Cat Camacho 15 Mar '18

15 Mar '18

Hello fellow neuroimagers! The Laboratory for Child Brain Development at the University of Pittsburgh is looking for a postdoctoral fellow starting this summer or fall. The LCBD employs multimodal neuroimaging to study child affective development from infancy to middle childhood. Please see the attached ad for more information. Thanks! Cat -- Maria Catalina Camacho PhD Student Center for Neuroscience Laboratory for Child Brain Development University of Pittsburgh mccamacho(a)pitt.edu 512-591-3741

1 0

Skull stripping error dataset
by Matthew Grecsek 15 Mar '18

15 Mar '18

I uploaded the datasets to the ftp site, does anyone have further advice regarding this issue? Both datasets are for the same subject for a longitudinal concussion study and fail for different reasons. matt1 - has "ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 errors" and fails with "CORRECTING DEFECT 51 (vertices=28380, convex hull=5261, v0=32826) XL defect detected..." never completing. matt2 - is leaving out large sections of brain despite various wsthresh adjustments (see thread below) I appreciate any assistance you can provide. All the best, -Matt Hi Matt no idea what that would happen. If you upload the dataset we will take a look cheers Bruce On Mon, 5 Mar 2018, Matthew Grecsek wrote: Following your advice below, it was clearly apparent that the output from the skull stripping step was missing a lot. I tried adjusting the -wsthresh flag from 50 -> 200 and it still left major parts of the brain out. I have a good quality mri and subject with no known anatomical abnormalities. The log file indicates "surface validation has detected possible Error" Does this suggest a more meaningful defect in the base image or something that can be corrected via other parameters or manual editing? Log file attached. Thanks, -Matt Bruce Fischl Fri, 02 Mar 2018 08:00:11 -0800 Hi Matt check the output of the skull stripping. This error usually means that too much (everything?) has been erased and no plausible cc could be found cheers Bruce On Thu, 1 Mar 2018, Matthew Grecsek wrote: My recon-all ended prematurely with the following message: final transformation (x=136.0, yr=-10.054, zr=-0.114): 0.98464 0.00200 -0.17457 15.51372; -0.00197 1.00000 0.00035 17.22442; 0.17457 0.00000 0.98464 -17.83761; 0.00000 0.00000 0.00000 1.00000; mri_cc: no WM voxels found with norm > 40 -- check skull stripping No such file or directory Linux centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux recon-all -s matt2 exited with ERRORS at Thu Mar 1 04:35:09 UTC 2018 I am running: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c My full log file is attached. Please let me know suggestions for correcting and continuing the process. Thanks, -Matt

1 0

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Freesurfer March 2018