thanks so much, it works and myelin maps look good now!
Lisa
On 8 June 2017 at 16:15, Harms, Michael <mha...@wustl.edu> wrote:
>
> ‘mkdir’ is telling you that the directory already exists. Normally that
> won’t abort a script, but it does in this case because of the “set -e” at
> the top of the script.
> The easy solution is to add the -p flag to the mkdir command, so that it
> is no longer considered an error if the directory already exists.
>
> 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 <(314)%20747-6173>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
> From: "Glasser, Matthew" <glass...@wustl.edu>
> Date: Thursday, June 8, 2017 at 8:30 AM
> To: Lisa Kramarenko <lisa.kramare...@gmail.com>
> Cc: Michael Harms <mha...@wustl.edu>, "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>
>
> Subject: Re: [HCP-Users] values in myelin maps
>
> 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>
> Date: Thursday, June 8, 2017 at 4:21 AM
> To: Matt Glasser <glass...@wustl.edu>
> Cc: "Harms, Michael" <mha...@wustl.edu>, "hcp-users@humanconnectome.org" <
> 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/00
> 3/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>
> 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> wrote:
>>
>>> Right she would want to comment out stuff that had already been done.
>>>
>>> Matt.
>>>
>>> From: "Harms, Michael" <mha...@wustl.edu>
>>> Date: Wednesday, June 7, 2017 at 12:50 PM
>>> To: Matt Glasser <glass...@wustl.edu>, Lisa Kramarenko <
>>> lisa.kramare...@gmail.com>
>>>
>>> Cc: "hcp-users@humanconnectome.org" <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 <(314)%20747-6173>
>>> St. Louis, MO 63110Email: mha...@wustl.edu
>>>
>>> From: "Glasser, Matthew" <glass...@wustl.edu>
>>> Date: Wednesday, June 7, 2017 at 11:55 AM
>>> To: Lisa Kramarenko <lisa.kramare...@gmail.com>, Michael Harms <
>>> mha...@wustl.edu>
>>> Cc: "hcp-users@humanconnectome.org" <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>
>>> Date: Wednesday, June 7, 2017 at 11:16 AM
>>> To: "Harms, Michael" <mha...@wustl.edu>
>>> Cc: Matt Glasser <glass...@wustl.edu>, "hcp-users@humanconnectome.org" <
>>> 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> 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 <(314)%20747-6173>
>>>> St. Louis, MO 63110Email: mha...@wustl.edu
>>>>
>>>> From: <hcp-users-boun...@humanconnectome.org> on behalf of Lisa
>>>> Kramarenko <lisa.kramare...@gmail.com>
>>>> Date: Wednesday, June 7, 2017 at 11:00 AM
>>>> To: "Glasser, Matthew" <glass...@wustl.edu>, "
>>>> hcp-users@humanconnectome.org" <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>
>>>> wrote:
>>>>
>>>>> thanks
>>>>>
>>>>> best,
>>>>> Lisa
>>>>>
>>>>> On 30 May 2017 at 16:37, Glasser, Matthew <glass...@wustl.edu> wrote:
>>>>>
>>>>>> Yes.
>>>>>>
>>>>>> Peace,
>>>>>>
>>>>>> Matt.
>>>>>>
>>>>>> From: Lisa Kramarenko <lisa.kramare...@gmail.com>
>>>>>> Date: Tuesday, May 30, 2017 at 9:31 AM
>>>>>>
>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>> Cc: "hcp-users@humanconnectome.org" <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>
>>>>>> 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>
>>>>>>> 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>
>>>>>>>> Date: Tuesday, May 30, 2017 at 8:59 AM
>>>>>>>>
>>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>>> Cc: "hcp-users@humanconnectome.org" <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-qu
>>>>>>>> ality-control-guide/freesurfer-quality-control-step-1-fix-pi
>>>>>>>> al-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>
>>>>>>>> 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>
>>>>>>>>> Date: Tuesday, May 30, 2017 at 8:49 AM
>>>>>>>>>
>>>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>>>> Cc: "hcp-users@humanconnectome.org" <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>
>>>>>>>>> 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>
>>>>>>>>>> Date: Tuesday, May 30, 2017 at 7:53 AM
>>>>>>>>>> To: Matt Glasser <glass...@wustl.edu>
>>>>>>>>>> Cc: "hcp-users@humanconnectome.org" <
>>>>>>>>>> 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>
>>>>>>>>>> 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> on behalf of Lisa
>>>>>>>>>>> Kramarenko <lisa.kramare...@gmail.com>
>>>>>>>>>>> Date: Monday, May 29, 2017 at 5:29 AM
>>>>>>>>>>> To: "hcp-users@humanconnectome.org" <
>>>>>>>>>>> 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
>>>>>>>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>> _______________________________________________
>>>> HCP-Users mailing list
>>>> 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. If you have received this email
>>>> in error, please immediately notify the sender via telephone or return
>>>> mail.
>>>>
>>>
>>>
>>
>
> ------------------------------
>
> 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. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
>
_______________________________________________
HCP-Users mailing list
HCP-Users@humanconnectome.org
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
