Freesurfer

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Re: [Freesurfer] Surface Problem
by Vionnet Laetitia 13 Apr '18

13 Apr '18

Dear freesurfer, I saw the issue below online and wondered whether it got solved? I have the “if: Missing file name.” error when testing my installation with recon-all -i sample-002.nii.gz -s bert -all attached my recon-all file. Thank you for your help and best regards, Laeitita -------------------- [Freesurfer] Surface Problem Z K zkaufman at nmr.mgh.harvard.edu <mailto:freesurfer%40nmr.mgh.harvard.edu?Subject=Re:%20%5BFreesurfer%5D%20Surface%20Problem&In-Reply-To=%3C253ef8e4-8ac6-18e9-86f7-f2945cbeba69%40nmr.mgh.harvard.edu%3E> Wed Jun 21 16:28:19 EDT 2017 * Previous message: [Freesurfer] Surface Problem <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052609.html> * Next message: [Freesurfer] FreeSurfer Boston Course Registration now open! <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052619.html> * Messages sorted by: [ date ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/date.html#5…> [ thread ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/thread.html…> [ subject ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/subject.htm…> [ author ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/author.html…> Search archives: Can you send me your recon-all script to my email address (not to the list). I suspect it has been modified. On 06/21/2017 02:04 PM, Michael Davies wrote: > Hello, i have been trying to regenerate the surface on one of my > subjects but keep having a problem where the terminal is saying there is > a missing file name. Do you have any suggestions please? > > > Kind regards, Michael > > > bash-4.1$ freesurfer_setup_freeview > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /usr/local/freesurfer_v6.0.0 > FSFAST_HOME /usr/local/freesurfer_v6.0.0/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/freesurfer_v6.0.0/subjects > MNI_DIR /usr/local/freesurfer_v6.0.0/mni > FSL_DIR /usr/local/fsl > bash-4.1$ cd /projects/pbic1030/Michael/subjects/Subj5/Subj5 > bash-4.1$ recon-all -autorecon-pial -s Subj5 > if: Missing file name. > bash-4.1$ > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer at nmr.mgh.harvard.edu<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > * Previous message: [Freesurfer] Surface Problem <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052609.html> * Next message: [Freesurfer] FreeSurfer Boston Course Registration now open! <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/052619.html> * Messages sorted by: [ date ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/date.html#5…> [ thread ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/thread.html…> [ subject ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/subject.htm…> [ author ]<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-June/author.html…> More information about the Freesurfer mailing list<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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Susceptibility artifact
by John Anderson 12 Apr '18

12 Apr '18

Dear Freesurfer experts, I would like t inquire if there is any tool or method in Freesurfer that can help to fix susceptibility artifacts in T1 image like attached Any suggestion is highly appreciated! John

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tksurkfer save error
by Evans, Jennifer (NIH/NIMH) [F] 12 Apr '18

12 Apr '18

Hi, This is a repost as I didn’t get a reply to the one I sent a few weeks ago. This error basically means I can’t automatically generate a webpage of all of the segmentation results. I getting an error when trying to save a tiff file using tksurfer on a linux machine via NoMachine v5.0.47. I’m running the ENIGMA QA pipeline which has a call similar to: tkfsurfer bert lh inflated. Then, trying to save the tiff either from the GUI or using their script doesn’t work and causes the error: pixel read error/resource temporarily unavailable. Is there a way to get this to work or is this a feature of using a virtual desktop? Thanks, Jen

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Data Analyst & Research Assistant Position(s) - Child Mind Institute (New York)
by Ting Xu 12 Apr '18

12 Apr '18

Child Mind Institute is seeking a Data Analyst to join our team. The Data Analyst’s role is to assist and support the acquisition, manipulation, and analysis of data, as well as the reporting results. In particular, our work includes: 1) support the preprocessing of large fMRI dataset in human and non-human primates, 2) maintain databases and imaging processing pipeline 3) test and develop new features (e.g., denoising, segmentation, etc.). 4) implement quality assurance protocols for imaging datasets. Reporting to the Research Scientist of the Center for the Developing Brain, this is an exempt, full-time positions located in our NYC headquarters. Responsibilities: Implementation, execution, and maintenance of fMRI imaging analysis pipelines in human and non-human primate datasets Exploration of novel software packages and problem-solving for issues with current and planned software packages Develop graphs, reports, and presentations of project results Mentoring of junior research staff in data analysis theory and implementation Perform basic statistical analyses for projects and reports Qualifications: Master’s degree or Bachelor’s degree with extensive neuroimaging research experience in neuroscience, computer science, mathematics, statistics or related areas Extensive neuroimaging experience in fMRI analysis and proficiency with one or more packages (e.g. FreeSurfer, AFNI, FSL, Workbench or SPM) Programming experience in one or more languages (e.g., Python, Matlab, R or similar platforms is required) Significant prior neuroimaging experience with more imaging and/or simulation modalities (e.g., DTI, EEG, MEG, TMS etc.) is a plus, but not required A passion for the Child Mind Institute mission To apply: https://workforcenow.adp.com/mdf/recruitment/recruitment.html?cid=371b930b-… -- Ting Xu, PhD Research Scientist Child Mind Institute childmind.org 445 Park Avenue (entrance on 56th Street) New York, NY 10022 Email: ting.xu(a)childmind.org

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Group Analysis Design Matrix
by David S Lee 12 Apr '18

12 Apr '18

Hi FreeSurfer Experts, I have two groups (Male and Female) and two covariates (Age and Weight). I want to test change of cortical thickness with age and weight, after removing effects of Group. In other words, is there an interaction between age and weight, regressing out the effects of groups. How can I set up my Design Matrix to test this? Thank you, -- David S. Lee Associate Research Specialist Center for Healthy Minds University of Wisconsin - Madison (608) 890-1115

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tksurkfer save error
by Evans, Jennifer (NIH/NIMH) [F] 12 Apr '18

12 Apr '18

Ok, thanks for the reply. It sounds like the ENIGMA folks need to updage their commands to use freeview. I'll try using ImageMajick's import as a workaround. Jen -------- Message: 11 Date: Thu, 12 Apr 2018 10:59:58 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] tksurkfer save error To: <freesurfer(a)nmr.mgh.harvard.edu>, Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> Message-ID: <834b362c-841b-5e86-cd3e-74b34ec33b76(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8"; format=flowed We are not really supporting tksurfer anymore. You can use freeview to save a png from the GUI. Ruopeng, is there a way to take a snap shot from the command line? On 04/12/2018 10:29 AM, Evans, Jennifer (NIH/NIMH) [F] wrote: Hi, This is a repost as I didn?t get a reply to the one I sent a few weeks ago.? This error basically means I can?t automatically generate a webpage of all of the segmentation results.? I getting an error when trying to save a tiff file using tksurfer on a linux machine via NoMachine v5.0.47.? I?m running the ENIGMA QA pipeline which has a call similar to: ?tkfsurfer bert lh inflated.? Then, trying to save the tiff either from the GUI or using their script doesn?t work and causes the error: pixel read error/resource temporarily unavailable. ??Is there a way to get this to work or is this a feature of using a virtual desktop? Thanks, Jen

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"preproc-sess" with intermediate volume
by David Sánchez Bestué 12 Apr '18

12 Apr '18

Dear all, I have a problem with the command: "preproc-sess" I wanted to use the Registration option to add an intermediate volume. The only documentation I could find about it was the one that appears with the command: "preproc-sess --help" Registration options -init-fsl : use fsl to initialize bbr registration -init-spm : use spm to initialize bbr registration (needs matlab) -init-header : use geometry to initialize bbr registration -bbr-int ifsd istem : use intermediate volume in sess/ifsd/RRR/istem I used the last flag in my line as follows: preproc-sess -s session_1 -fsd bold -surface self lhrh -mni305 -fwhm 5 -per-run -bbr-int ifsd istem I got this error: ERROR: could not determine file for ifsd/001/istem It seems that the path is not working but I do not why. The relevant paths are this: session_1/bold/001/f.nii session_1/ifsd/001/istem/orig.mgz Any help would be really appreciated! Thank you all Bests, David

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Roundness of a surface label
by Jonathan DuBois 12 Apr '18

12 Apr '18

Hi, I was wondering if there was any existing freesurfer script to calculate the roundness and/or the perimeter of a surface label? If anyone has ideas on how to calculate this, I would appreciate it. Thanks, Jonathan

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MCR
by John Absher 12 Apr '18

12 Apr '18

Hi, I was pleased to learn freesurfer runs with the standalone matlab runtime, and installed this on CentOS7. It seems to be working well. I noticed that there's also a version of spm12 that runs using this runtime, "with limitations." Two questions: 1. Are there freesurfer limitations using this runtime that can be overcome by having the full matlab version installed? 2. Can I use the same runtime I've already installed for freesurfer to run spm12, or will I need a new one? Thanks, John John R. Absher, MD, FAAN GHS Neurosciences jabsher(a)ghs.org<mailto:jabsher@ghs.org> 864-350-6655 (mobile)

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Re: [Freesurfer] mri_vol2surf: unable to compare volume maps
by Douglas N. Greve 12 Apr '18

12 Apr '18

Hi Srishti, you will need to be much more specific to allow me to help you. mni152_subject is not a file that can be input to recon-all (it should be a dicom or nifti or mgz). If you use the same input to recon-all that you used to view it in spm, then the FS output should align with your map. On 04/12/2018 10:41 AM, srishti goel wrote: > mni152_subject is the file that has been used for recon-all. Our > collaborators had run recon-all with that file so we did not do it > again. As far as the 'MNI template' is concerned, I didn't do that > part of the analysis so I am unsure which specific file it is, but it > MNI 152. > > 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@email.unc.edu> > skype: srishti.goel12 > > > On Thu, Apr 12, 2018 at 10:28 AM, Douglas N. Greve > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote: > > What is the "MNI template" that you are using. I mean an exact file > used. Did you use this file when you ran recon-all? > > > On 04/12/2018 10:23 AM, srishti goel wrote: > > Yeah, I am unsure where to go from here as well. So the results > can be > > viewed in SPM and on the MNI template space itself, since SPM > > typically does not have a problem showing multiple images in > different > > sizes. > > > > 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@email.unc.edu> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> > > skype: srishti.goel12 > > > > > > On Thu, Apr 12, 2018 at 10:11 AM, Douglas N. Greve > > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>>> > wrote: > > > > When you use bbregister, it is expecting the input nii file to > > represent > > the actual anatomy of the subject, so it does not surprise > me that it > > does not work that well. I'm not sure what to do about this > because a > > meta analysis image will never have decent anatomy. In > theory, it > > should > > be already in alignment with the mni152, but this is > trickier than it > > seems. How do you usually view the results? In FSL or SPM? > Do you view > > them on an anatomical image? > > > > > > On 04/12/2018 09:03 AM, srishti goel wrote: > > > Hi Douglas, > > > > > > The negative_allsocial_proportion.nii file has actually been > > converted > > > from a vmp file - 'negative_allsocial.vmp'. We used > neruoelf to > > > convert the vmp file, option - 'export to analze' and > 'export to > > > nifti'. The original vmp file represent the results of a > > meta-analysis. > > > > > > Let me know if that helps or you would need more information. > > > > > > Thanks! > > > > > > 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 > <mailto:srishtig@email.unc.edu> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>>> > > > skype: srishti.goel12 > > > > > > > > > On Wed, Apr 11, 2018 at 11:30 PM, Douglas Greve > > > <dgreve(a)mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu> > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>> > > wrote: > > > > > > how was negative_allsocial_proportion.nii created? > > > > > > > > > On 4/11/18 9:14 PM, srishti goel wrote: > > >> Hi, > > >> > > >> I used bbregister to register: > > >> bbregister --mov negative_allsocial_proportion.nii --s > > >> mni152_subject --bold --lta register.lta > > >> and then viewed it using: > > >> tkregisterfv --mov negative_allsocial_proportion.nii > --reg > > >> register.lta --surfs > > >> It doesn't look great but it still looks okay (Screenshot > > attached). > > >> Then I also used lta in tkregisterfv, as: > > >> tkregisterfv --mov negative_allsocial_proportion.nii > --reg > > >> register.lta --s mni152_subject --surfs --reg > reg.deleteme.dat > > >> In this file, the volume map still lies outside the > surface. > > >> Could you please help me resolve this issue. > > >> I tried using register.lta file in the mri_vol2surf > but the > > >> overlay map doesn't show up again. > > >> Thanks! > > >> > > >> 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@email.unc.edu> > > <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>>> > > >> skype: srishti.goel12 > > >> > > >> > > >> On Tue, Apr 10, 2018 at 11:50 PM, Douglas Greve > > >> <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>> > > wrote: > > >> > > >> don't use --init-rr ( you don't need to spec an > init in > > >> version 6) > > >> > > >> > > >> On 4/10/18 9:48 PM, srishti goel wrote: > > >>> When I run bbregister, it gives me an error. > Attached > > is the > > >>> register.dat.log file for it. > > >>> Error: > > >>> > > >>> reading source > './tmp.bbregister.91068/template.nii'... > > >>> > > >>> mri_robust_register.bin: only pass single frame > MRI source > > >>> ./tmp.bbregister.91068/template.nii. > > >>> > > >>> > > >>> No such file or directory > > >>> > > >>> > > >>> Any help is greatly appreciated! > > >>> > > >>> > > >>> 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@email.unc.edu> > > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> > > >>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>>> > > >>> skype: srishti.goel12 > > >>> > > >>> > > >>> On Tue, Apr 10, 2018 at 11:07 AM, Douglas Greve > > >>> <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>> > > wrote: > > >>> > > >>> They are not in registration. Try running > > bbregister to > > >>> create a registration file (lta), then pass > the lta to > > >>> tkregisterfv instead of --regheader > > >>> > > >>> > > >>> On 4/9/18 11:49 PM, Bruce Fischl wrote: > > >>>> How did you generate the registration? And give > > us the > > >>>> details of what you are trying to register > > >>>> Cheers > > >>>> Bruce > > >>>> > > >>>> On Apr 8, 2018, at 2:55 PM, srishti goel > > >>>> <23srishtigoel(a)gmail.com > <mailto:23srishtigoel@gmail.com> > > <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com>> > > >>>> <mailto:23srishtigoel@gmail.com > <mailto:23srishtigoel@gmail.com> > > <mailto:23srishtigoel@gmail.com <mailto:23srishtigoel@gmail.com>>>> wrote: > > >>>> > > >>>>> Hi Bruce, > > >>>>> > > >>>>> Thanks so much for pointing that out, I > totally > > missed > > >>>>> that part. > > >>>>> > > >>>>> Also, the registration definitely isn't > appropriate. > > >>>>> Could someone please guide me how to > correct this > > >>>>> problem. I have attached a screenshot of > how it > > looks > > >>>>> like currently. > > >>>>> > > >>>>> > > >>>>> <Screen Shot 2018-04-08 at 2.53.33 PM.png> > > >>>>> > > >>>>> 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@email.unc.edu> > > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> > > >>>>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>>> > > >>>>> skype: srishti.goel12 > > >>>>> > > >>>>> > > >>>>> On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl > > >>>>> <fischl(a)nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>> > > >>>>> <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>>> wrote: > > >>>>> > > >>>>> Hi Srishti > > >>>>> > > >>>>> the directory you are in doesn't > matter. YOu > > >>>>> either need to set SUBJECTS_DIR in the > > >>>>> environment, or use --sd <SUBJECTS_DIR> to > > specify the > > >>>>> directory that contains your subjects. I > > think you > > >>>>> can also give it the full path to a target > > volume > > >>>>> if you want, but maybe Doug can > comment as he > > >>>>> knows this stuff better than I do > > >>>>> > > >>>>> cheers > > >>>>> Bruce > > >>>>> > > >>>>> > > >>>>> > > >>>>> On Sun, 8 Apr 2018, srishti goel wrote: > > >>>>> > > >>>>> When I type this > command:tkregisterfv --mov > > >>>>> negative_allsocial_proportion.nii --regheader --s > > >>>>> mni152_subject --surfs --reg > > reg.deleteme.dat > > >>>>> > > >>>>> It gives me the error: cannot find > > mni152_subject. > > >>>>> Although I clearly checked that the > > directory > > >>>>> from which I am submitting this > command > > has the > > >>>>> mni152_subject directory within which there > > >>>>> are all the other required > directories such > > >>>>> as: mri, > > >>>>> stats, surf, scripts, etc. > > >>>>> > > >>>>> I am unsure what is happening here. > > >>>>> > > >>>>> > > >>>>> 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@email.unc.edu> > > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>> > > >>>>> <mailto:srishtig@email.unc.edu > <mailto:srishtig@email.unc.edu> > > <mailto:srishtig@email.unc.edu <mailto:srishtig@email.unc.edu>>> > > >>>>> skype: srishti.goel12 > > >>>>> > > >>>>> > > >>>>> On Thu, Apr 5, 2018 at 12:49 PM, > Douglas N. > > >>>>> Greve <dgreve(a)mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > > <mailto:dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> > > >>>>> <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu> > > <mailto:dgreve@mgh.harvard.edu > <mailto:dgreve@mgh.harvard.edu>>>> wrote: > > >>>>> Those commands look ok. My suspicion > > >>>>> goes to the use of --regheader. See > > >>>>> whether the registration is ok with > > >>>>> > > >>>>> tkregisterfv --mov > > >>>>> negative_allsocial_proportion.nii --regheader --s > > >>>>> mni152_subject --surfs --reg > > reg.deleteme.dat > > >>>>> > > >>>>> > > >>>>> On 04/05/2018 08:34 AM, srishti > > goel wrote: > > >>>>> > Hi, > > >>>>> > > > >>>>> > I am trying to compare my volume > > maps > > >>>>> > > > (negative_allsocial_proportion.nii) to > > >>>>> someone else's > > >>>>> > (SN_like_cortical_lh.nii.gz) who > > have > > >>>>> it on a surface > > >>>>> > (mni152_subject). So I used the > > steps > > >>>>> for mri_vol2surf command as > > >>>>> > follows: > > >>>>> > > > >>>>> > Commands: > > >>>>> > mri_vol2surf --src > > >>>>> negative_allsocial_proportion.nii --regheader > > >>>>> > mni152_subject --hemi lh --o > > >>>>> ./neg_allsocial_lh.nii --projfrac 0.5 > > >>>>> > Then to view it: > > >>>>> > tksurfer mni152_subject lh inflated > > >>>>> -overlay ./neg_allsocial_lh.nii > > >>>>> > -overlay SN_like_cortical_lh.nii.gz > > >>>>> -fthresh 0.5 > > >>>>> > > > >>>>> > Everything ran fine and we > > didn't get > > >>>>> any error but then while viewing > > >>>>> > the files we could not see our map > > >>>>> (neg_allsocail_lh.nii) on the > > >>>>> > surface. This file seemed to > > work fine > > >>>>> as it is not an empty file when > > >>>>> > I checked the file size. > > However, when > > >>>>> we view it using tksurfer it > > >>>>> > does not show up as a highlighted > > >>>>> portion on the surface. The > > >>>>> > SN_like_cortical_lh.nii.gz file > > shows > > >>>>> up just fine. > > >>>>> > > > >>>>> > Could someone please help me figure > > >>>>> out what might have gone wrong here. > > >>>>> > > > >>>>> > Thanks so much! > > >>>>> > > > >>>>> > > > >>>>> > > > >>>>> > > > _______________________________________________ > > >>>>> > Freesurfer mailing list > > >>>>> > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> > > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >>>>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >>>>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > >>>>> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >>>>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > >>>>> > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >>>>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >>>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > >>> <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >>> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >>> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > >> <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > >> <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > >> > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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> > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline>> > > > <http://www.partners.org/complianceline > <http://www.partners.org/complianceline> > > <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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > <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@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@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > >

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