You could delete that or make the mkdir a conditional if it doesn’t already exist.
Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Thursday, June 8, 2017 at 4:21 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps I am sorry, I have made a mistake in the mail above. It seems that the Pipeline ended in the end of the "FreeSurferHiresPial.sh" script and not the Intermediate recon-all steps. It ended after Reading surface file /Users/user/Desktop/003/T1w/003/surf/rh.pial.postT2.pass2 Applying linear registration transform 1.000 0.000 0.000 0.000; 0.000 0.000 -1.000 0.350; 0.000 1.000 0.000 0.000; 0.000 0.000 0.000 1.000; INFO: trgsubject = srcsubject Saving target data mkdir: ribbon.postT2.pass1: File exists So as I understand it, the only part that didn't finish are the Final Recon-all Steps. Should I delete the folder "ribbon.postT2.pass1" before running the pipeline the way I described above, so that it can be created again (and the ribbon files moved there) and the pipeline can end? Sorry for naive questions and thanks again. Lisa On 8 June 2017 at 09:59, Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote: I wasn't sure about the exact hacking process and just naively commented out lines 133-167 in the FreeSurfer script, so that I started with recon-all -subjid $SubjectID -sd $SubjectDIR -autorecon2 -nosmooth2 -noinflate2 -nocurvstats -nosegstats -openmp ${num_cores} ${seed_cmd_appendix} (with brainmask and wm being edited) It ran without problems, but stopped after saying "mkdir: ribbon.postT2.pass1: File exists" in the Intermediate Recon-all Steps. So it was rewriting everything up to this point but for some reason stopped there. Nevertheless, seeing that surfaces seemed to have been regenerated, I tried to run PostFreeSurfer and apart from the warnings ("annot file: /Users/user/Desktop/003/T1w/003/label/lh.BA.annot MRISreadAnnotationIntoArray: vertex index out of range: 146448 i=00190519, in_array_size=146066) it went without error and my myelin map looks good now. What do you think? Can I use it or should I change something else so that the complete pipeline finishes? Thanks! Lisa On 7 June 2017 at 19:53, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Right she would want to comment out stuff that had already been done. Matt. From: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Date: Wednesday, June 7, 2017 at 12:50 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps I haven’t thought this all through, but I think that one of the main things you’d need to hack is to be able to make use of an already existing FS output. Currently, I believe that re-running the pipeline will simply overwrite any existing FS files, as if you were running FS de-novo. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>> Date: Wednesday, June 7, 2017 at 11:55 AM To: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>>, Michael Harms <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps Hi Lisa, I was going to suggest that you hack the pipeline yourself if you are comfortable with that. You might try starting at line 167 of the FreeSurfer pipeline to incorporate the brainmask edits (the WM edits might not be needed then). As for the control points, I don’t know enough about that to advise you so you’ll need to consult the FreeSurfer documentation to see where to add them in. The main things we do to modify the recon-all script is to assist with brain masking, to fine tune the white surface to be placed based on high res data, and place the pial surface based on highres T1w and T2w data using the script modules. The white surface tuning happens in between –white and –smooth2 whereas the pial surface tuning happens between -pial and -surfvolume on this table: http://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV5.3 Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Wednesday, June 7, 2017 at 11:16 AM To: "Harms, Michael" <mha...@wustl.edu<mailto:mha...@wustl.edu>> Cc: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps so that means if something went wrong with the skull strip and surfaces during the FreeSurfer Pipeline there is no other alternative than to exclude these subjects? On 7 June 2017 at 18:04, Harms, Michael <mha...@wustl.edu<mailto:mha...@wustl.edu>> wrote: Unfortunately, the HCP Pipelines do not currently support rerunning FreeSurfer after editing. It is on our list of “things to do” to add that functionality. cheers, -MH -- Michael Harms, Ph.D. ----------------------------------------------------------- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134 660 South Euclid Ave.Tel: 314-747-6173<tel:(314)%20747-6173> St. Louis, MO 63110Email: mha...@wustl.edu<mailto:mha...@wustl.edu> From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Wednesday, June 7, 2017 at 11:00 AM To: "Glasser, Matthew" <glass...@wustl.edu<mailto:glass...@wustl.edu>>, "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps Dear Matthew, I have now manually edited brainmask.gmz ans wm.gmz to remove dura that was still mistaken for a surface. Now I am not sure from which step to re-run these participants. 1. Do I understand it correctly that after replacing brainmask.gmz and wm.gmz in the <subjid>/mri I need to start the FreeSurfer Pipeline after the step "# Generate brain mask" (meaning starting with the step "# Call recon-all to run most of the "-autorecon2" stages, but turning off smooth2, inflate2, curvstats, and segstats stages")? 2. Do I need to use any additional flags in the autorecon after my intervention? 3. I also created some control points to fix missing white matter. Should I put the control.dat file in the <subjid>/tmp folder? Will FreeSurfer see the file automatically or should I add some flag for it? thanks a lot for your help! Lisa On 30 May 2017 at 16:38, Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote: thanks best, Lisa On 30 May 2017 at 16:37, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Yes. Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 9:31 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps do I find the files I should inspect in the {subject_id}/T1w/{subject_id}/mri/ folder? On 30 May 2017 at 16:28, Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> wrote: ok. so basically just go through recon-all output and manually correct whatever might have gone wrong? best, Lisa On 30 May 2017 at 16:13, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: I would look for locations in which the FreeSurfer aseg is clearly labeling things outside of the brain as grey or white matter. Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 8:59 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps Alright, thanks for the quick reply! Should I look for some specific problem with the surfaces which is to be fixed? I mean I imagine a lot of things can go wrong with a surface, so that I need to know what exactly to fix? Or is it something more general like this: http://sites.bu.edu/cnrlab/lab-resources/freesurfer-quality-control-guide/freesurfer-quality-control-step-1-fix-pial-surface/ ? And does it look like it affect both pial and white matter surfaces, so that both need to be fixed? Sorry for the naive questions and thanks again. On 30 May 2017 at 15:51, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Fat saturation reduces the intensity of the fat within the bone marrow, which reduces the chance that FreeSurfer will mistake this fat for white matter. You would need to have this on during acquisition. As for how to fix the surfaces after the fact, I would look at FreeSurfer’s documentation. Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 8:49 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps Yes, this is data of the lab I am in. I assume that I don't have fat saturation as I have never heard about it before... If I understand correctly it can't be done post-hoc after acquisition and should have been done during scanning? Other patients from the same batch (acquired the same way) don't have this problem. What would be the way to fix the surfaces manually? Thanks a lot! On 30 May 2017 at 15:42, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: Are these of your own data? Do you have fat sat on in your T1w? This looks like most likely surface errors because of not using fat sat and you would need to exclude these subjects or fix the surfaces manually. Peace, Matt. From: Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Tuesday, May 30, 2017 at 7:53 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>> Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] values in myelin maps Thanks! Another question I have concerning myelin maps is the following: when I was doing quality control I noticed that some of them look rather weird (see screenshot). Why are some areas grey? And I presume the fact that the values in this grey area are negative, indicates that something is wrong... And are the black parts normal (they still have positive values)? Do you have an idea of what to do? Thanks a lot! Lisa On 29 May 2017 at 15:55, Glasser, Matthew <glass...@wustl.edu<mailto:glass...@wustl.edu>> wrote: They are the ratio of the T1w/T2w images and are a relative measure of myelin content. See this publication for more details: http://www.jneurosci.org/content/31/32/11597.short Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Lisa Kramarenko <lisa.kramare...@gmail.com<mailto:lisa.kramare...@gmail.com>> Date: Monday, May 29, 2017 at 5:29 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [HCP-Users] values in myelin maps Hello, I am not sure what exactly are the values shown for the myelin maps. E.g. on the screenshot the values are 0.998 to 1.771. I understand that higher values mean higher myelination and vice versa, but what do they mean exactly? Thanks! Lisa _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. 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