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30134 discussions

Recon reprocessing control points error
by Sarah Finnegan 09 Nov '16

09 Nov '16

Hi Bruce, Thanks for your email. I have uploaded the two examples. The first subj001_fs.zip has the control points added but has not been rerun yet. The second subj001_fs_cp.zip has been rerun and the segmentation looks incorrect. Thanks for your input! Sarah ________________________________________

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Area after fsaverage resample
by Lachlan Strike 09 Nov '16

09 Nov '16

Dear FreeSurfer Developers I have a question regarding the area measures for subjects following registration to fsaverage (produced through the qcache flag – lh/rh.area.fsaverage.mgh). What do the values for each vertex represent? Is it correct to state that these measures are in mm2, or are these measures now somehow relative to the corresponding vertex values within fsaverage? Best regards Lachlan

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mri_gtmpvc error: failed tissue type check
by Donatas Sederevicius 09 Nov '16

09 Nov '16

Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replacing 18 ERROR: CheckSegTissueType() tissue type for seg 29 Left-undetermined not set Failed tissue type check gtmseg was run as: gtmseg --s ID247 and completed without errors. mri_gtmpvc was run as: mri_gtmpvc --i /projects/PET/processed/ID247/ID247_PIBStatic.nii.gz --psf 2 --no-rescale --seg /projects/PET/recon/ID247/mri/gtmseg.mgz --reg /projects/PET/processed/ID247/PET2MRI.lta --default-seg-merge --o /projects/PET/processed/ID247/gtmpvcYES.output/SGTM/non_scaled --save-input --km-ref 8 47 --km-hb 11 12 13 50 51 52 How could this problem be solved? Thank you. Best regards, Donatas

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nuisance dichotomous variables
by Dominic Dwyer 09 Nov '16

09 Nov '16

Dear FS experts, Sorry for my confusion here, but I'm wondering why dichotomous nuisance variables (e.g., gender) can't be used in qdec? I was thinking that if it uses a generalized linear model then it should be ok? I read other posts and understand why discrete factors can't be used with more than 2 levels, but was thinking that dichotomous variables should be different. NB. we're trying to run a simple two group comparison, but we two dichotomous variables that we want to control for. Many thanks for your help, Dom -------------------------------------------------------------------- Dom Dwyer, PhD Psychiatry & Psychotherapy LMU Munich A: Nußbaumstr. 7, Munich, 80336 E: dominic.dwyer(a)med.uni-muenchen.de T: +49 (0)89 4400 55880

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Recon reprocessing control points error
by Sarah Finnegan 09 Nov '16

09 Nov '16

Hi there, I am using freesurfer v5.3.0 to recon some 7T structural scans. I have been adding some control points to compensate for poor temporal lobe contrast, something that has worked just fine many times before. However, now when rerunning the recon process as follows: recon-all -autorecon2-cp -autorecon3 -subjid <name> It looks like the reprocessing has not taken the control points into account at all, and actually has changed the segmentation in areas that were previously fine. My control.dat file is in the subjid/tmp folder and is populated correctly so I assume it should be able to be located. Can anyone offer any advice on what might be going on? The same error is also being experienced by a colleague here. Thanks a lot! Sarah Finnegan Nuffield Department of Clinical Neurosciences University of Oxford, John Radcliffe Hospital Oxford, OX3 9DU Email: sarah.finnegan(a)stcatz.ox.ac.uk<mailto:sarah.finnegan@stcatz.ox.ac.uk>

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Longitudinal Stream on HCP Data
by Timothy Hendrickson 08 Nov '16

08 Nov '16

Aww thank you for clarifying Michael. I definitely misread Matthew's post. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Fwd: [HCP-Users] HCP to FreeSurfer Resampling
by Timothy Hendrickson 08 Nov '16

08 Nov '16

FreeSurfer experts, I am attempting to resample HCP data into FreeSurfer space with the following how to document: https://wiki.humanconnectome. org/display/PublicData/HCP+Users+FAQ. <https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ> I believe I have resampled the GIFTI file into fs_average space, however I am running to problems visualizing it in freeview or tksurfer. Please see the error message in the forwarded message below? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ---------- Forwarded message ---------- From: Timothy Hendrickson <hendr522(a)umn.edu> Date: Tue, Nov 8, 2016 at 8:51 AM Subject: Re: [HCP-Users] HCP to FreeSurfer Resampling To: Timothy Coalson <tsc5yc(a)mst.edu> Cc: "hcp-users(a)humanconnectome.org" <HCP-Users(a)humanconnectome.org> Hi Tim, Thank you for taking a look at my script, I really appreciate it. I am now running into another problem. After re-sampling into fs_average space I am attempting to visualize that file as an overlay in tksurfer or freeview (freesurfer visualization tools) however I receive the following error: *mriseadGIFTIfile: mris is NULL! found when parsing file rh.43242.32k_TJH_fsavg.func.gii*. I know that freesurfer can handle GIFTI file so that is not the problem. I wonder if the GIFTI file was created incorrectly... Any advice? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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Re: [Freesurfer] mapping ROI to surface space
by Bruce Fischl 08 Nov '16

08 Nov '16

Hi Derek I'll cc the FS list so others can answer. It depends on the reason the holes exist. It also depends on the size of the holes. The dev version of mri_label2labels supports morphological close operations. It takes an integer parameter which should be about the radius of the holes you would like to fill in. Note that this will also fill in some concavities in the boundary of the label. cheers Bruce On Tue, 8 Nov 2016, Andrews, Derek wrote: > Hi Bruce, > > Apologies for contacting you directly but I’m not sure if my message is > getting through to the list. > > I have gotten ahold of the dev version of mri_label2label. > > Currently I have a .w file that I need to “fill in the holes” on. Could > you please specify the steps I will need to take to make my .w file an > acceptable input for mri_label2label, and any recommendations you may have > for the value of N for the —close flag. > > Any help you could provide would be appreciated. > > Best, Derek > > > > > ________________________________________ > Derek Sayre Andrews, MSc > PhD Candidate > > The Sackler Institute for Translational Neurodevelopment > Department of Forensic and Neurodevelopmental Sciences > Institute of Psychiatry, Psychology & Neuroscience, King's College London > > Telephone: +44 (0)20 7848 5701 > Email: Derek.Andrews(a)kcl.ac.uk > > > > > > On 28/10/2016 15:53, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: > >> Hi Derek >> >> I think the dev version of mri_label2label supports >> open/close/dilate/erode >> operations: >> >> mri_label2label --help >> USAGE: mri_label2label.bin >> >> --srclabel input label file >> >> --erode N erode the label N times before writing >> --open N open the label N times before writing >> --close N close the label N times before writing >> --dilate N dilate the label N times before writing >> . >> . >> . >> >> if your version doesn't have these operations let us know and we can get >> you an updated one >> >> cheers >> Bruce >> >> >> >> On Fri, 28 Oct 2016, >> Andrews, Derek wrote: >> >>> Hi Bruce, >>> >>> As always thank you for your prompt reply. >>> >>> For the morphological close operation, would you suggest using mris_fill >>> on the surface ROI I created and then running mri_vol2surf again on the >>> volume output by mris_fill? >>> >>> Best, Derek >>> >>> >>> ________________________________________ >>> Derek Sayre Andrews, MSc >>> PhD Candidate >>> >>> The Sackler Institute for Translational Neurodevelopment >>> Department of Forensic and Neurodevelopmental Sciences >>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>> London >>> >>> Telephone: +44 (0)20 7848 5701 >>> Email: Derek.Andrews(a)kcl.ac.uk >>> >>> >>> >>> >>> >>> On 28/10/2016 14:54, "Bruce Fischl" <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>>> p.s. you could remove many/most of these holes using a morphological >>>> close operation >>>> On Fri, 28 Oct 2016, Andrews, Derek wrote: >>>> >>>>> Hello Freesurfer Developers and Community, >>>>> >>>>> I am looking to map a ROI.nii based on the MNI152 template to the >>>>> fsaverage >>>>> pial surface. >>>>> >>>>> I have used the following commands >>>>> >>>>> Bbregister ‹s fsaverage ‹mov MNI152.nii ‹reg register.dat ‹init-fsl >>>>> ‹12 >>>>> ‹t1 >>>>> >>>>> Then >>>>> >>>>> mri_vol2surf ‹src ROI.nii ‹out ROI.mgh ‹srcreg register.dat ‹hemi lh >>>>> >>>>> The ROI appears to be in the right place however is very blotchy. >>>>> Have I >>>>> missed a step? Or is this correct? >>>>> >>>>> See bellow a picture of the ROI highlighted in FSL and in tksurfer >>>>> after >>>>> mapped using the above. >>>>> >>>>> Thank you for your support, >>>>> >>>>> Best, Derek >>>>> >>>>> [IMAGE] >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> _______________________________________________________________________ >>>>> __ >>>>> ___ >>>>> >>>>> Derek Sayre Andrews, MSc >>>>> PhD Candidate >>>>> >>>>> The Sackler Institute for Translational Neurodevelopment >>>>> >>>>> Department of Forensic and Neurodevelopmental Sciences >>>>> >>>>> Institute of Psychiatry, Psychology & Neuroscience, King's College >>>>> London >>>>> >>>>> Telephone: +44 (0)20 7848 5701 >>>>> Email: Derek.Andrews(a)kcl.ac.uk >>>>> >>>>> >>>>> >>>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> >>>> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail. >>>> nm >>>> >>>> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek >>>> .a >>>> >>>> ndrews%40kcl.ac.uk%7C65ef7af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16 >>>> b8 >>>> >>>> 3c724071654356%7C0&sdata=liaieNpnjB7M4w9favIeZ9B0ZrooUbfDThLvJxmbcuo%3D& >>>> re >>>> served=0 >>>> >>>> >>>> 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 >>>> >>>> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.pa >>>> rt >>>> >>>> ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C65e >>>> f7 >>>> >>>> af2f2c1455a461a08d3ff3a0395%7C8370cf1416f34c16b83c724071654356%7C0&sdata >>>> =% >>>> 2F%2Fl3dvHGeXDJCkpHGWdvv9sI59QW76kFK%2FK1HdUQZnE%3D&reserved=0 . 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://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.n >>> mr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek >>> .andrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c1 >>> 6b83c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3 >>> D&reserved=0 >>> >>> >>> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nm >> r.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=01%7C01%7Cderek.a >> ndrews%40kcl.ac.uk%7C619839454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b8 >> 3c724071654356%7C0&sdata=b7RxteOygtLeOXwEqb7jklBy8UF4yYIW2P08all9jKQ%3D&re >> served=0 >> >> >> 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 >> https://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.part >> ners.org%2Fcomplianceline&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C61983 >> 9454aa24e2abb5b08d3ff423c1d%7C8370cf1416f34c16b83c724071654356%7C0&sdata=y >> glzZIazWf12gfszA3LPiOPVUl9m2jppoYC8oUjsrlI%3D&reserved=0 . 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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Longitudinal Stream on HCP Data
by Timothy Hendrickson 08 Nov '16

08 Nov '16

Hi Freesurfer/HCP experts, I am curious if there is a way to incorporate HCP data (i.e. myelin maps) into the FreeSurfer processing stream. Matthew Glasser mentioned in a post on the HCP mailing list about a month back that this is being actively worked on by FreeSurfer: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html. <http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html> Are there any workflows or development versions that I can download in order to perform something like this. Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay)

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recon-all steps question
by miracle ozzoude 08 Nov '16

08 Nov '16

Hello Freesurfer, I have couple of questions. While going through the frequently asked questions on your page http://freesurfer.net/fswiki/UserContributions/FAQ I came across a question regarding how to integrate a skull stripped from another problem into freesurfer (using recon-all -autorecon1 -noskullstrip -s subjid ----> create a symbolic link from T1.mgz to brainmask.auto.mgz and another like from brainmask.auto.mgz to brainmask.mgz ------> after run the finall stages of recon-all: recon-all -autorecon2 -autorecon3 -s subjid). First question, isn't T1.mgz, brainmask.auto.mgz and brainmask.mgz created during skull stripping? why are they present if I included the "-no skullstrip" flag? Second question, where do I insert my already skull stripped data in the symbolic link? Last question, the final stages of recon-all doesn't include skull stripping, how can I be sure my skull stripped data was incorporated into the freesurfer recon-all process? Best, Paul

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