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Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation
by Gabor Perlaki 26 Feb '18

26 Feb '18

Does anybody else have a comment on the experienced artefact <petzinger.gabor(a)gmail.com>

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Re: [Freesurfer] Hippocampal Subfield Error
by Iglesias Gonzalez, Eugenio 26 Feb '18

26 Feb '18

Dear Theo, Can you please provide us with the command you executed, and the complete output logs? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "AKUDJEDU, THEOPHILUS" <T.AKUDJEDU1(a)nuigalway.ie> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, 26 February 2018 at 12:39 To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Hippocampal Subfield Error Hi All, I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield segmentation but exited with errors. The content of the recon-all.error file is below. SUBJECT CHRM2001 DATE Sun Feb 25 00:34:13 GMT 2018 USER 15233963 HOST psych-sl03 PROCESSOR x86_64 OS Linux Linux psych-sl03 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ /opt/ohpc/pub/apps/freesurfer/6.0.0/bin/recon-all PWD /home/15233963/freesurfer/SUBJECTS/CHRM2001/label CMD mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab CHRM2001 rh white Will be glad if you can provide guidance. Cheers Theo _______________________________ Theophilus Akudjedu BSc, MSc, PhD Candidate Room 202 Comerford Suite, Clinical Science Institute, Department of Psychiatry, National University of Ireland, Galway Phone: +353 838329602 Email: t.akudjedu1(a)nuigalway.ie<mailto:t.akudjedu1@nuigalway.ie> rasningo(a)gmail.com<mailto:rasningo@gmail.com> [mage removed by sender.]

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-make versus -all for edits
by Maksimovskiy, Arkadiy 26 Feb '18

26 Feb '18

Dear Experts, I was wondering if someone might be able to help me understand what the difference is between the two commands below. It seems that they can be used interchangeably, because I can forsee a situation in which one might not remember which command to run and also have done several types of corrections. Or would the former (-make) method only work on with 1 edits? Thanks, Arkadiy If you cannot remember which command to run, use the -make flag. Recon-all will automatically begin at whichever point in the processing stream you made your edits. recon-all -make all -subjid <subject> If you have corrected several types of errors, it is recommended that you re-run recon-all from the beginning, to ensure that none of your edits were left out. (Running from autorecon1 will not save you much time) recon-all -all -subjid <subject> -- Arkadiy L. Maksimovskiy, Ph.D. Postdoctoral Research Fellow McLean Imaging Center, McLean Hospital Department of Psychiatry, Harvard Medical School

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Hippocampal Subfield Error
by AKUDJEDU, THEOPHILUS 26 Feb '18

26 Feb '18

Hi All, I tried to run a subject through FreeSurfer 6.0 for hippocampal Subfield segmentation but exited with errors. The content of the recon-all.error file is below. SUBJECT CHRM2001 DATE Sun Feb 25 00:34:13 GMT 2018 USER 15233963 HOST psych-sl03 PROCESSOR x86_64 OS Linux Linux psych-sl03 3.10.0-327.36.3.el7.x86_64 #1 SMP Mon Oct 24 16:09:20 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.580.2.16 2017/01/18 14:11:24 zkaufman Exp $ /opt/ohpc/pub/apps/freesurfer/6.0.0/bin/recon-all PWD /home/15233963/freesurfer/SUBJECTS/CHRM2001/label CMD mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab CHRM2001 rh white Will be glad if you can provide guidance. Cheers Theo _______________________________ Theophilus Akudjedu BSc, MSc, PhD Candidate Room 202 Comerford Suite, Clinical Science Institute, Department of Psychiatry, National University of Ireland, Galway Phone: +353 838329602 Email: t.akudjedu1(a)nuigalway.ie<mailto:t.akudjedu1@nuigalway.ie> rasningo(a)gmail.com<mailto:rasningo@gmail.com> [https://ci6.googleusercontent.com/proxy/b9-AoNc-V0v85TZ_pj6puJTgX7uWBNlZdoh…]

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Re: [Freesurfer] TRACULA registration
by Gabriela Longo 23 Feb '18

23 Feb '18

Yes, got it. But in these text files, the first line is already "#!ascii label, vox2ras=scanner". It seems the problem is before the -stat step because I got many NaN. My impression is that the tracts inter-subjects are not well aligned. I also verified the registration, I will send the pictures: 1) dfifit_FA with MNI, that looks good: [image: Imagem inline 1] 2) merged_avg33_mni_bbr.mgz x dtifit_FA.nii.gz, that also looks good: [image: Imagem inline 2] 3) and then, when I checked the merged_avg33_mni_bbr.mgz with MNI, it looks incorrect: [image: Imagem inline 3] 2018-02-23 15:21 GMT-05:00 Gabriela Longo < gabrielalongo.radiologia(a)gmail.com>: > In these text files, the first line is already "#!ascii label, > vox2ras=scanner". > > It seems the problem is before the -stat step because I got many NaN. My > impression is that the tracts inter-subjects are not well aligned. > I also verified the registration, I will send the pictures: > > 1) dfifit_FA with MNI, that looks good: > [image: Imagem inline 1] > > 2) merged_avg33_mni_bbr.mgz x dtifit_FA.nii.gz, that also looks good: > [image: Imagem inline 2] > > 3) and then, when I checked the merged_avg33_mni_bbr.mgz with MNI, it > looks incorrect: > [image: Imagem inline 3] > > 2018-02-23 14:11 GMT-05:00 Yendiki, Anastasia <AYENDIKI(a)mgh.harvard.edu>: > >> So you may have been caught in that transition. The paths that you load >> into trackvis with the –w option are text files. Change the first line in >> those files to: >> #!ascii label, vox2ras=scanner >> >> When you do that and load the paths into freeview again, do they show up >> inside the brain? >> >> From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Gabriela >> Longo <gabrielalongo.radiologia(a)gmail.com> >> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Date: Friday, February 23, 2018 at 1:34 PM >> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >> Subject: Re: [Freesurfer] TRACULA registration >> >> Hi Anastasia, >> >> thanks for your email. >> I did the whole analysis in the developmental version, even the -stat. >> >> Thanks, Gabriela >> >> 2018-02-23 13:21 GMT-05:00 Yendiki, Anastasia <AYENDIKI(a)mgh.harvard.edu>: >> >>> Hi Gabriela – Any chance that you generated the paths with an older >>> version of TRACULA, and viewed them in a newer version of freeview? There >>> was a change in freeview at some point, in terms of the header that it >>> expects those path files to have. This change happened between the 5.3 and >>> 6.0 freesurfer releases, so if you ran TRACULA from the 5.3 release and >>> used freeview from 6.0 or from a patched version that you downloaded in >>> between 5.3 and 6.0, they may be incompatible. This would explain the >>> outside the brain part. Now beyond that it seems that there's more >>> strangeness going on, but let’s figure that part out first. >>> >>> Thanks, >>> a.y >>> >>> From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Gabriela >>> Longo <gabrielalongo.radiologia(a)gmail.com> >>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> >>> Date: Friday, February 23, 2018 at 11:25 AM >>> To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> >>> Subject: [Freesurfer] TRACULA registration >>> >>> Hi, >>> >>> I processed some subjects in TRACULA for a longitudinal evaluation. >>> I registered all of them in the MNI template (set doregmni = 1 >>> set mnitemp = $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz). >>> >>> I checked the registration of my dtifit_FA.bbr.nii.gz with the MNI of >>> all subjects. >>> However, when I performed the group analysis, I got more NaN than >>> expected and I checked the images and the results are outside the MNI >>> template (I am sending a picture). >>> >>> I went back and checked the registration of the paths. Despite the dtifit_FA.bbr.nii.gz >>> is correctly registered in the MNI, the paths aren't. >>> >>> I am struggling here to find solutions. I really appreciate any insight >>> to help me to solve this issue. >>> >>> Thanks in advance, >>> >>> Gabriela Longo >>> >>> [image: Imagem inline 2] >>> >>> >>> _______________________________________________ >>> 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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FreeSurfer Labels To Diffusion Toolkit/TrackVis
by Katherine Damme 22 Feb '18

22 Feb '18

Hello Everyone, I would like to use the FreeSurfer labels for fMRI and DTI in graph theory analyses. I am attempting to use UMPC <https://github.com/jbrown81/umcp> to generate the graphs, which requires that the diffusion tensor imaging be in .dtk form. However, I have been struggling to get the FreeSurfer labels into the .dtk space. While I have found this <https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms>website suggesting a method for moving from the dtk space to FreeSurfer, it doesn't appear to be a reversible process. Leading me to ask: 1. Is there a way to generate graphs from TRACULA? or 2. How can I transform the labels or dlabels into dtk space? Thank you for any help on this topic! Kate Damme

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Update: asymmetric parcellation error
by Dijkshoorn, A.B.C. (Aicha) 22 Feb '18

22 Feb '18

Dear Freesurfer developers, When I was troubleshooting my data I came across an odd parcellation error that I can not place. When looking at the reconstructed surface parcellation (freeview -f {$subject}/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ --viewport 3d) I noticed that in a large proportion of my subjects the parcellated errors are not placed correctly. Moreover, the error mostly seems to apply to the right cortex and not the left. I adjusted foto's for visual information. I already checked the brain mask.mgz file and the rh.white and rh.pial surfaces I cannot find any segmentation errors either. Do you have any idea what could have gone wrong and how I can correct for this? Kind regards, Aicha

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asymmetric parcellation error
by Dijkshoorn, A.B.C. (Aicha) 22 Feb '18

22 Feb '18

Dear Freesurfer developers, When I was troubleshooting my data I came across an odd parcellation error that I can not place. When looking at the reconstructed surface parcellation (freeview -f {$subject}/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ --viewport 3d) I noticed that in a large proportion of my subjects the parcellated errors are not placed correctly. Moreover, the error mostly seems to apply to the right cortex and not the left. I adjusted foto's for visual information. Do you have any idea what could have gone wrong and how I can correct for this? Kind regards, Aicha

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Freesurfer equivalent to fslmaths?
by Zimmerman, Jared 22 Feb '18

22 Feb '18

Hi all, Is there an equivalent of fslmaths in Freesurfer? I would like to add two scalar value images (.mgh files) that are registered to the fsaverage6 surface but I’m not seeing an obvious way to do it. Right now I’m reading the images into Matlab to add them, but this is a bit inconvenient because what I would like to do is smooth an image by a small amount, add the original image back to it, then smooth again marginally and iterate until I get to a target fwhm. Since I can’t smooth inside Matlab this necessitates writing out a temp image for each smoothing step then reading it back into Matlab for the adding. Obviously this is a solvable problem, but as someone only marginally proficient in Matlab it’s something I’d like to avoid, plus it seems like a lot of I/O for this task. A little more detail on my data and what I’m trying to do: The scalar images I’m working with are network confidence maps, basically like the spatial maps from an ICA dual-regression. I want to combine the confidence maps together into a hard partition and write it to an annot file, but I want to smooth them first. I’m concerned, however, that smoothing is going to bias the parcellation against small network parcels and in favor of large network parcels because in each confidence map the small parcels will be surrounded by lots of zeros (does this make sense?). To correct for this, my idea was to iteratively smooth by small amounts and to add the original confidence values (or some fraction of them) back to the smoothed map after each iteration so that regions of high confidence with a small/narrow spatial spread do not become diluted by the smoothing and don’t get taken over by larger high confidence regions in nearby networks. One final question would be how to smooth on a surface without resampling. Right now I’m using mri_surf2surf and smoothing when I resample to the native mesh, but if I take the above approach I would not want to resample at each smoothing step. Could I just use mri_surf2surf with –srcsubject and –trgsubject pointing to the same subject? Thanks, Jared ____________________________ Jared P. Zimmerman jaredz(a)pennmedicine.upenn.edu Neuroscience Graduate Student Oathes Lab University of Pennsylvania

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Longitudinal analysis using SLURM {Disarmed}
by Backhausen, Lea 22 Feb '18

22 Feb '18

Dear FS experts, I am trying to do a longitudinal analysis of around 250 adolescents with up to 4 data points each. Given the complexity I would like to use the long_submit_jobs script which is described here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts Unfourtunately it does only run on launchpad and I would do the analyses with SLURM using bash system. Has anybody adopted the script so i will run with SLURM or does anybody know where I should look to get information on this? I have little scripting experience so any help would be greatly appreciated! Best, Lea Backhausen, B.Sc. Research assistant Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie Tel. +49 (0)351 458-7166 Fax +49 (0)351 458-5754 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://www.uniklinikum-dresden.de<https://deref-web-02.de/mail/client/kXc4jbFBtdU/dereferrer/?redirectUrl=htt…> Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. med. Peter C. Scriba USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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