Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30061 discussions

Re: [Freesurfer] Postdoctoral Scholar in Neuroimaging of Epilepsy and Brain Tumors
by Marshall, Anisa 07 Dec '17

07 Dec '17

Dear all, We are seeking a full-time postdoctoral scholar to work with a multidisciplinary team of scientists on projects related to the use of multimodal imaging for improving cognitive and health outcomes in patients with epilepsy and brain tumors. Our team includes full-time faculty from Psychiatry, Radiology, Neurosciences, and Radiation Oncology at UC San Diego. This group of researchers and clinical investigators are primarily focused on integrating research imaging tools and genetic information into the clinical work flow to directly and immediately improve patient outcomes. The scholar will work closely with other postdoctoral fellows, medical residents, graduate students, research assistants, and faculty members to help develop methods, analyze structural, diffusion, and functional (fMRI) imaging data, prepare manuscripts and assist with grant applications. The fellow should have strong programming and writing skills, experience in neuroimaging or a related field, and a strong interest in pursuing an academic career path. Applicants with a strong background in bioengineering, cognitive science, and/or experience in machine learning and other multidimensional data integration approaches are encouraged to apply. Location: UCSD Center for Multimodal Imaging and Genetics (CMIG) UCSD Center for Translational Imaging and Precision Medicine (CTIPM) Start date: Flexible, but no later than Spring/Summer 2018 This position is located at the UCSD CMIG, which is located on the East Medical Campus in La Jolla, CA in the Altman CTRI. The fellow will share an office with another postdoctoral fellow and have direct access to two 750 GE systems. Please send application to Dr. Carrie McDonald (camcdonald(a)ucsd.edu<mailto:camcdonald@ucsd.edu>). Kind regards, Anisa ---------- Anisa Marshall, MS Neuroimaging Research Associate Center for Multimodal Imaging and Genetics (CMIG) UC San Diego Office phone: (858) 246-0291 a6marshall(a)ucsd.edu<mailto:a6marshall@ucsd.edu>

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Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
by Taylor, Johnmark 07 Dec '17

07 Dec '17

Thanks once again for all the help on this. I am running the GLM in native space, typically so that I can get the beta values to use in an MVPA analysis. So it sounds like if you specify per-run motion-correction and registration, and don't tell it to resample to anything (e.g., the MNI brain or the surface), then there's no guarantee that the voxels will properly line up if you want to do, for instance, a single-subject GLM in the subject's native space? So in this case, per-session motion correction would be better so that all the functional volumes in the session are registered properly? > Thank you, this is very helpful! A few quick followup questions: > > 1) If you don't specifically tell preproc-sess what space to resample > too (e.g., by using the "-surface" or "-mni305" flags), does it > automatically resample to the subject's anatomical volume, then? I don't think it will do anything if you don't specify > > 2) If fmc.nii.gz is already registered to the subject's volume, then > how come a registration file has to be specified when visualizing GLM > results using tksurfer? If fmc.nii.gz is already resampled to > anatomical space, then surely any GLM contrasts should be as well, no? fmc is not registered to the anatomical, it is registered to the template. The template is registered to the anat through the registration file. The data are still in the native functional space. > > 3) If per-run motion correction and registration is specified in > pre-proc sess, then there will be a different functional-->structural > transformation for each run, correct? Correct > If this is the case, then when visualizing session-wide GLM results > using tksurfer, which registration file should be specified when > loading up the overlay, since there'll be a different registration > file for each run? In what space are you doing the GLM? Usually, the raw data are resampled onto the surface (eg, fmc.fsaverage.lh.sm05.nii.gz), and the GLM is done in this spae.so no registration is needed. > > Apologies for these (probably basic) questions, I just want to make > sure I am crystal-clear on what preproc-sess is doing. > > Cheers, and many thanks, > > JohnMark

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PET partial volume correction:mri_gtmpvc error
by Herranz Muelas, Elena 07 Dec '17

07 Dec '17

Dear Freesurfers, I am trying to apply partial volume correction to my PET images, following the steps explained in the PetSurfer wiki. When I run the mri_gtmpvc command, it works fine for most of the subjects but for some of them I get the following error message: /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space Loading input /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz done loading input 1 frames $Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $ setenv SUBJECTS_DIR /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3 cd /autofs/space/alicudi_002/users/mscat/users/elena/scripts/PVC mri_gtmpvc --i /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.nii.gz --reg /autofs/space/alicudi_002/users/mscat/users/caterina/MR-PET/MSPET06/PET/PET-space/SUVR.reg.lta --psf 6 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/gtmpvc.output sysname Linux hostname alicudi.nmr.mgh.harvard.edu machine x86_64 user ehmuelas vgthresh 0.001000 nReplace 18 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 40 avail.processors, using 1 Creating output directory /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/gtmpvc.output Loading seg for gtm /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.mgz Loading seg ctab /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.ctab Reading /autofs/space/alicudi_002/users/mscat/users/caterina/3T/recons_fsv5.3/MSPET06_recon/mri/gtmseg.lta Replacing 18 Pruning ctab Checking tissue type ERROR: CheckSegTissueType() tissue type for seg 64 Right-F3orb not set Failed tissue type check And the command line that I ran: mri_gtmpvc --i $path_to_suvr/SUVR.nii.gz --reg $path_to_suvr/SUVR.reg.lta --psf 6 --seg gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx .01 --o $path_to_recon/$subj"_recon"/gtmpvc.output Could you please help me out with this? Many thanks in advance! Elena

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Freeview problem: ROIs showing in wrong slice when loaded with certain volumes
by Sims, Sara A 06 Dec '17

06 Dec '17

Hello, I am having an issues with freeview ROIs. When I use the command line to load the orig and the ROIs by themselves they display correctly, however when I display the orig volume and the volume versions of the ROIs- the label ROIs suddenly change to be in the wrong plane. I have done this same thing before and this hasn’t happened. Right now I am having to load just the orig and ROI labels then run the command within freeview to load the label volumes to get it to display all the images at the same time correctly. I would like to do it all in one command line at the same time. Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin(a)uab.edu

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Stats test
by Daya P 06 Dec '17

06 Dec '17

Hi all, I have a group of 31 subjects scanned at two time points.I have mean BOLD activation for each region of aparc2009. I would like to test if there is any significant difference in terms of mean BOLD activation between time point 1 and time point 2 in each region, and then introduce thickness as a covariate to see if that explains the differences. Is there any statistical test that you can recommend? Thank you, Daiana

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Re: [Freesurfer] Clarification about "Per-Run" Motion Correction and Registration in Preproc-Sess
by Taylor, Johnmark 06 Dec '17

06 Dec '17

Thank you, this is very helpful! A few quick followup questions: 1) If you don't specifically tell preproc-sess what space to resample too (e.g., by using the "-surface" or "-mni305" flags), does it automatically resample to the subject's anatomical volume, then? 2) If fmc.nii.gz is already registered to the subject's volume, then how come a registration file has to be specified when visualizing GLM results using tksurfer? If fmc.nii.gz is already resampled to anatomical space, then surely any GLM contrasts should be as well, no? 3) If per-run motion correction and registration is specified in pre-proc sess, then there will be a different functional-->structural transformation for each run, correct? If this is the case, then when visualizing session-wide GLM results using tksurfer, which registration file should be specified when loading up the overlay, since there'll be a different registration file for each run? Apologies for these (probably basic) questions, I just want to make sure I am crystal-clear on what preproc-sess is doing. Cheers, and many thanks, JohnMark On Mon, Dec 4, 2017 at 3:20 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. Re: mri_binarize (Douglas N Greve) > 2. Re: Clarification about "Per-Run" Motion Correction and > Registration in Preproc-Sess (Douglas N Greve) > 3. Re: freesurfer design (Douglas N Greve) > 4. Re: subcortical structures volume (Douglas N Greve) > 5. Re: mri_vol2surf wrong hemisphere (Douglas N Greve) > 6. Re: Concatenating .mgh surface space functional MRI runs > (Douglas N Greve) > 7. Re: QDEC and comparing two conditions (Douglas N Greve) > 8. Re: Combining parcellated regions within an atlas? > (Douglas N Greve) > 9. Re: Overlaying multiple results onto one surface (Douglas N Greve) > 10. recon edit error (Nicole Orme) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 4 Dec 2017 12:30:33 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_binarize > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <9d91f7ea-a55b-cd78-2b55-687cf2078a8b(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > you can do it in two steps. First, use mri_binarize to create a mask of > the structutures you want. Then use mri_mask to apply the mask to the > aparc.DKT file > > > On 12/03/2017 07:44 AM, John Anderson wrote: > > Dear FS experts, > > I want to use mri_binarize to create (binarized and free of CSF and > > ventricles) mask from "aparc.DKTatlas+aseg". How can I substract CSF > > and ventricles from teh atlas using mri_binarize? > > > > Thanks > > John > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 2 > Date: Mon, 4 Dec 2017 12:32:00 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Clarification about "Per-Run" Motion > Correction and Registration in Preproc-Sess > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <813a5a08-d27e-a2a6-8472-66f998aaa4a2(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > > > On 12/03/2017 06:35 PM, Taylor, Johnmark wrote: > > Hello, > > > > A few quick questions about the "Per-Run" option in preproc-sess. I > > understand that in this option, each run's images are registered to > > the middle timepoint of that run, rather than the first timepoint of > > the first run. I was wondering, though: > > > > 1) Why is this the preferred option instead of per-session? > The interpolation is less if it is done on a per-run basis, and the > registration might be better > > 2) If motion-correction is only done internally to each run, then > > wouldn't between-run motion throw things off if you wanted to do a GLM > > spanning the whole scanning session (although I assume it'd be fine > > for single-run GLMs)? What ensures that the images line up properly > > between runs? > That is why we resample into the group atlas space (eg, fsaverage) or > the self anatomical space so that all the runs are aligned. > > > > Thank you very much, > > > > JohnMark > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 3 > Date: Mon, 4 Dec 2017 12:33:46 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] freesurfer design > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <daca7a06-f2e5-09a1-f05b-7e24204bc8cb(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > In theory, this is just a two "group" analysis. Search the wiki for FSGD > to get examples. You can include covariates, but you must use a DOSS > model when running mri_glmfit > > > On 12/04/2017 04:41 AM, Dijkshoorn, A.B.C. (Aicha) wrote: > > > > Dear freesurfer group, > > > > I have two questions: > > > > Can I compare one patient with a created control group in Freesurfer > > on the following outcome measures: cortical thickness, brain volume > > and gyrification? If so, how can you?visualise that? > > When you do the cortical analysis with freesurfer?can?you?account > > for?covariates in the statistical model (before visualisation)? > > > > Kind regards, > > > > Aicha Dijkshoorn > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 4 > Date: Mon, 4 Dec 2017 12:39:55 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] subcortical structures volume > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <cb08cf9c-9912-c39e-8979-ace86c2ea5f4(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=UTF-8; format=flowed > > Yes, you should take those into account. Not sure what you mean by > "which stat analysis". > > > On 12/01/2017 07:50 PM, ??? wrote: > > Hi professor, > > > > ? ?I am using Freesurfer 6.0 and get the volume of subcortical > > structures. I want to get the relationship between age and volume. I > > only have one group, is it necessary to take gender and ?eTIV as a > > covariate? If it is necessary, Which statistical analysis should be used? > > ? ?I really appreciate your help. Thanks a lot. > > > > Sincerely, > > Zheng > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 5 > Date: Mon, 4 Dec 2017 12:46:27 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] mri_vol2surf wrong hemisphere > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <4ddc19b2-a602-5560-9cf5-0d7ff60baca5(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > How do you know what is right and left in the volume? > > > On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote: > > > > Hi, > > > > I have a strange issue I can't figure out. I am currently trying to > > use the parcellation from Gordon et al. 2014 > > (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs > > for the frontoparietal network. They provided a volume of the > > parcellation in MNI152 space for public use. I took this volume and > > applied the mri_vol2surf command to it to create 2 overlays of the > > parcels, 1 for each hemisphere. The code was: > > > > mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage > > --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh > > > > mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage > > --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh > > > > The code ran, but the LH parcels in the volume were transferred to the > > RH on the surface and vice versa. This is a problem since the > > parcellation is not symmetric across hemispheres.This is not a problem > > with the volume either as I looked at it overlayed with the MNI152 > > brain in fslview and saw that the parcels were on the correct > > hemisphere. Another problem is that 1 of the frontoparietal parcels, > > number 24, was not found on the surface of either hemisphere after > > turning it to a surface. I don't know why this would be the case since > > there are all cortical parcels. > > > > I have also tried this with a volume ROI that is only located on the > > left hemisphere. After running essentially the same vol2surf command > > as above, the ROI only appeared on the RH surface. I am using > > mri_vol2surf from Freesurfer v6.0.0 > > > > > > Any help would be greatly appreciated. Thank you! > > > > Best, > > Matthew Defenderfer > > > > > > *Matthew K. Defenderfer B.S. |?Graduate Research Assistant* > > > > Graduate Biomedical Sciences|Neuroscience > > > > UAB?|?The University of Alabama at Birmingham > > > > Laboratory of Kristina Visscher, PhD > > > > Department of Neurobiology > > > > CIRC 111 | C: (865) 805-6389 > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 6 > Date: Mon, 4 Dec 2017 12:47:18 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Concatenating .mgh surface space functional > MRI runs > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <6e8749cf-4be8-04c4-17a2-5b6a96d7a520(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > mri_concat file1 file2 ... --o concatfile.mgh > > > On 11/30/2017 01:28 PM, Abisan - wrote: > > Hi Freesurfer experts, > > > > I want to concatenate multiple preprocessed fMRI runs in the form of > > .mgh freesurfer surface space files (2-D matrices vertexes * > > time_frames). Is there a tool that can do this easily, or do you have > > other recommendations how to do this? > > > > Thank you! > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 7 > Date: Mon, 4 Dec 2017 12:50:20 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] QDEC and comparing two conditions > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <e9ec8a98-c015-0050-9ede-fa91008f215c(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > If you want to do a conjunction, you can run mri_concat with the > --conjunct option (see --help for more details). If you want to look at > simple overlap, you can threshold each sig map (mri_binarize), then > combine them together something like > > fscalc map2.bin.nii.gz mul 2 add map1.bin.nii.gz -o overlap.nii.gz > > overlap will be > > 1 for map1 only > > 2 for map2 only > > 3 for both > > > On 11/30/2017 01:46 PM, Rizvi, Batool wrote: > > > > Hi ? I?m still wondering what would be the best method to perform the > > mentioned steps. Additionally, would mri_compute_overlap provide > > output related to spatial overlap and difference, that we?re looking > > for? Is it possible to do this with thickness, or maybe not ? because > > it doesn?t consider area? Just wondering, as we only performed QDEC > > using thickness so far. > > > > Thanks so much, > > > > Batool > > > > *From:* Rizvi, Batool > > *Sent:* Tuesday, November 28, 2017 3:16 PM > > *To:* freesurfer(a)nmr.mgh.harvard.edu > > *Subject:* QDEC and comparing two conditions > > > > Hi FreeSurfer experts, > > > > We calculated the correlation between thickness two different > > behavioral conditions using QDEC. We now want to compare the spatial > > overlap and difference in thickness-correlation between the two > > behavioral conditions. We would like to do this both visually as well > > as statistically. Is there an option to do this either in QDEC or in > > the command line? > > > > Thanks for your time! > > > > Batool > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 8 > Date: Mon, 4 Dec 2017 12:57:18 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Combining parcellated regions within an > atlas? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <ab6331c8-0280-b9e4-df9f-456c0285439f(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=utf-8; format=flowed > > You can break the annotation into separate labels > (mri_annotation2label), then merge the ones you want into a single label > (mri_mergelabels), then recombine them into an annotation > (mris_label2annot) > > > On 11/29/2017 10:03 PM, Michiko H. wrote: > > Hi Freesurfer Experts, > > > > I was wondering what the best way of combining regions within a > > parcellation? For example, in the Schaefer 2017 functional atlas, > > there are regions such as: > > > > 7Networks_LH_DorsAttn_FEF_1 ? ? ? ? ? 0 118 22 ?0 > > 7Networks_LH_DorsAttn_FEF_2 ? ? ? ? ? 0 119 17 ?0 > > 7Networks_LH_DorsAttn_FEF_3 ? ? ? ? ? 0 119 18 ?0 > > 7Networks_LH_DorsAttn_FEF_4 ? ? ? ? ? 0 119 19 ?0 > > 7Networks_LH_DorsAttn_PrCv_1 ? ? ? ? ?0 119 20 ?0 > > 7Networks_LH_DorsAttn_PrCv_2 ? ? ? ? ?0 119 21 ?0 > > > > If I would like to combine all the DorsAttn_FEF areas into 1 node and > > DorsAttn_PRCv areas into another, what is the best way to do this? I > > currently have an image that has been parcellated using this atlas > > that was brought into volumetric space. I would need to have a > > transformed re-parcellated file and a corresponding color LUT file. > > > > Would appreciate any help, thank you! > > > > Best, > > Michiko > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 9 > Date: Mon, 4 Dec 2017 12:59:10 -0500 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > Subject: Re: [Freesurfer] Overlaying multiple results onto one surface > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <98c037e5-25b1-18f7-1325-5f9dac45c652(a)nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > I think you would need to figure out what such a combination would look? > like. Eg, you could have a separate label for each possible combination > contrasts above threshold, though this would create a combinatorial > explosion. > > > On 11/29/2017 02:48 PM, Nguyen, Tin wrote: > > > > Hello, > > > > I have been running different analyses through QDEC GUI for different > > covariates that describe a similar construct, for instance: > > > > ?Model A: (cortical thickness) ~ (covariate 1) + (nuisance factors) > > > > ?Model B: (cortical thickness) ~ (covariate 2) + (nuisance factors) > > > > ?Model C: (cortical thickness) ~ (covariate 3) + (nuisance factors) > > > > ?Model D: (cortical thickness) ~ (covariate 4) + (nuisance factors) > > > > ?Model E: (cortical thickness) ~ (covariate 5) + (nuisance factors) > > > > As a result, I have 5 different brain images to illustrate each of the > > 5 models for their corresponding covariates. Is there way to overlay > > all 5 of the images onto a common space to have 1 representative brain > > image? This is to show overlapping effects, or the lack thereof, of > > the covariates. > > > > Thank you. > > > > -Tin > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > ------------------------------ > > Message: 10 > Date: Mon, 4 Dec 2017 14:17:39 -0500 > From: Nicole Orme <nicoleaorme(a)gmail.com> > Subject: [Freesurfer] recon edit error > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <8378B2B8-EB83-4C7D-8A54-E3ED470DC7A3(a)gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hello FreeSurfer Developers, > > I have been editing my MRI images using the recon edit tool. I > have been editing the white matter so it does not include grey matter. When > I click shift to remove the extra voxels included in white matter they are > removed, which is what supposed to happen. Where I?m encountering a problem > is sometimes I?ll have clicked the shift but are not holding the mouse down > so it seems as if the entire image gets selected. I?ve attached a > screenshot. I don?t know how to reverse this. It then will have all the > images selected. > > If you could help me that would be great! > > Nicole >

2 1

Infant Atlas
by li ki 06 Dec '17

06 Dec '17

2 1

new paper published
by Bruce Fischl 06 Dec '17

06 Dec '17

Hi All we just published a paper on 3D microscopic imaging of connectivity and architecture: https://www.sciencedirect.com/science/article/pii/S105381191730825X if you are interested. cheers Bruce

3 2

Infant Atlas
by li ki 06 Dec '17

06 Dec '17

Hi experts, We are presently involved in a project for analyzing MRI data of 1-3 year old children using FreeSurfer. We cannot find a correct infant atlas. From online search, I know that an infant atlas is being developed which will be integrated into FreeSurfer in the future. （link https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/ [https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/pmc-logo-share.png]<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/> A FreeSurfer-compliant consistent manual segmentation of ...<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4332305/> www.ncbi.nlm.nih.gov We present a detailed description of a set of FreeSurfer compatible segmentation guidelines tailored to infant MRI scans, and a unique data set of manually segmented ... ） Can I know when this will be available? If not soon, is there any other methods for us to generate an infant(kid) atlas? Also I know there are infant atlas from UNC(http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-a…, how can I use this atlas in Freesurfer? Free Softwares ― IDEAgroup<http://www.med.unc.edu/bric/ideagroup/free-softwares/unc-infant-0-1-2-atlas…)> www.med.unc.edu Free Softwares developed by IDEA lab are collected here for research use. Best, Lemon

1 0

freeview abort
by ~永夜~ 05 Dec '17

05 Dec '17

Hi experts, When I use xshell to connect our Ubuntu system，freeview aborts without any other complaint.wade@DL:/$ freeview Abort (core dumped) after dealed with suggestion on https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2017-September/05399… still cannot work. wade@DL:/$ /sbin/ldconfig -N -v $(sed 's/:/ /' <<< $LD_LIBRARY_PATH) | grep libvtkverdict.so /sbin/ldconfig.real: Can't stat /lib/i686-linux-gnu: No such file or directory /sbin/ldconfig.real: Can't stat /usr/lib/i686-linux-gnu: No such file or directory /sbin/ldconfig.real: Path `/usr/lib/nvidia-367' given more than once /sbin/ldconfig.real: Path `/usr/lib32/nvidia-367' given more than once /sbin/ldconfig.real: Path `/lib/x86_64-linux-gnu' given more than once /sbin/ldconfig.real: Path `/usr/lib/x86_64-linux-gnu' given more than once /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkpng.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkmetaio.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtklibxml2.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkCommon.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkftgl.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkImaging.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkIOTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkNetCDF.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libMapReduceMPI.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGenericFiltering.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkIO.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtksqlite.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkVolumeRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkCommonTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGraphics.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkalglib.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkWidgetsTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkImagingTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkHybrid.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkRendering.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtksys.so.5.6 is not a symbolic link libvtkverdict.so.5.6 -> libvtkverdict.so.5.6.0 /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGenericFilteringTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkWidgets.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkHybridTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkDICOMParser.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkzlib.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkexoIIc.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkVolumeRendering.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkGraphicsTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libmpistubs.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkproj4.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkFiltering.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/freesurfer/lib/vtk/lib/vtk-5.6/libvtkRenderingTCL.so.5.6 is not a symbolic link /sbin/ldconfig.real: /usr/local/cuda-8.0/targets/x86_64-linux/lib/libcudnn.so.5 is not a symbolic link /sbin/ldconfig.real: /lib/i386-linux-gnu/ld-2.19.so is the dynamic linker, ignoring /sbin/ldconfig.real: /lib/x86_64-linux-gnu/ld-2.19.so is the dynamic linker, ignoring /sbin/ldconfig.real: Cannot stat /usr/lib32/nvidia-367/libOpenGL.so: No such file or directory /sbin/ldconfig.real: /lib32/ld-2.19.so is the dynamic linker, ignoring /sbin/ldconfig.real: /libx32/ld-2.19.so is the dynamic linker, ignoring libvtkverdict.so.5.8 -> libvtkverdict.so.5.8. Can I get the tar of the vtk library or any help is highly appreciated! Thanks you! Wade

1 0

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