Freesurfer

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30063 discussions

dmrirc.tutorial problem
by lanbo Wang 13 Nov '17

13 Nov '17

Dear experts, I try to run trac-all -bedp -c dmrirc.tutorial, but error shows like this, then stop: INFO: SUBJECTS_DIR is /HD4/DTI INFO: Diffusion root is HD4/DTI Actual FREESURFER_HOME /HD2/freesurfer WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.2nd/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.3rd/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.4th/dmri [mtobia@localhost DTI]$ trac-all -bedp -c dmrirc.tutorial INFO: SUBJECTS_DIR is /HD4/DTI INFO: Diffusion root is HD4/DTI Actual FREESURFER_HOME /HD2/freesurfer WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.2nd/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.3rd/dmri WARN: Running bedbostx locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 HD4/DTI/DBK08.4th/dmri Thanks for your patient and help. All best, Lanbo Wang

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Unrealistic "mri_fdr" Results
by Hossein Rejali 13 Nov '17

13 Nov '17

Hi, Sorry I am very new to this field, forgive me for ignorance. I am trying to do multiple comparison correction on my data set that I ran through mri_glmfit. I am currently using mri_fdr as a means for multiple comparison correction. The problem I am having now is that after running mri_fdr, the output surface overlays are completely zero. This seems very unlikely from the clusters I had, well at least hopefully unlikely. Below I have posted part of the code for my analysis that is calling the mri_fdr function: mri_fdr --fdr $thresh --${sign} --i $SUBJECTS_DIR/Group_Analysis/R1_projdist0.${dist}.fwhm${fwhm}/GLM_Output/${hemi}.Output/Diff-con-scz-R1/sig.mgh nomask $SUBJECTS_DIR/Group_Analysis/R1_projdist0.${dist}.fwhm${fwhm}/GLM_Output/${hemi}.Output/Corrected/FDR-Output-${sign}-thresh${thresh}.mgh Sorry for the mess but essentially, I am running though a couple of for loops that runs through variable values posted below: for thresh in 0.5 0.1 0.05 0.01 for sign in neg pos for hemi in lh rh for fwhm in15 20 for dist in 2 I am hoping there is something wrong with the way I am calling mri_fdr, any help would be greatly appreciated. Kind Regards, Hossein Rejali

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Re: [Freesurfer] functional to anatomical registration
by Douglas N Greve 13 Nov '17

13 Nov '17

Hi David, please post to the list ... answers below On 11/13/2017 01:48 PM, David Beeler wrote: > Hi Doug, really helpful thanks! > So if I want all the motion corrected functional data across runs to be aligned with a downsampled version of my anatomical, is it better to run preproc-sess with -per-session or should I do -per-run and then map each functional to anatomical without resampling using: > mri_vol2vol --reg register.dof6.lta --mov fmcpr.nii.gz --fstarg \ --o > fmcpr.new.vox2ras.nii.gz --no-resample > and then run selxavg3-sess on the fmcpr.new.vox2ras.nii.gz in each run > folder? I've heard motion correction with -per-run is better but I > don't understand why... can you explain? Oh, if you want to do it that way, then you would not use the --no-resample (that just changes the geometry in the header). per-run registers and resamples to the middle time point, meaning that there is generally less interpolation. You should add --fstarg orig.mgz This will have it sample into the 1mm orig space. This will create a very largefile. If you want to downsample the anat, you can run mri_convert --downsample 2 2 2 orig.mgz orig.ds2.mgz and then --fstarg orig.ds2.mgz > Further, I don't get how selxavg3-sess chooses its input. If I first > do preproc-sess with -per-run, do my transformation to downsampled > anatomical space (as described above), and then run selxavg3-sess with > the -no-preproc flag, what volume will selxavg3-sess use by default? I > assume it will search the run folders for fmcpr.nii.gz (because using > f.nii.gz would defeat the purpose of doing motion correction in the > first place), but is there a flag I could use to tell selxavg3-sess to > use my transformed fmcpr.new.vox2ras.nii.gz as input instead? Should I > just rename fmcpr.new.vox2ras.nii.gz to fmcpr.nii.gz and then > selxavg3-sess will take it automatically? When you create your analysis, you should put -funcstem fmcpr.new.vox2ras > Thanks again! > David > PS is this the correct way to respond to threads on this mailing list > so that the thread is maintained? > On 11/8/17 5:57 PM, David Beeler wrote: > > Hi freesurfer people, > > I'm trying to understand preprocessing a little better, especially > registration of functional data to anatomical space. I am > currently running everything in the volume, doing motion > correction per-run and then pooling all the runs in the session > together for the first level analysis.As far as I can tell, > running preproc-sess with -per-run takes the rawfunctional data > (f.nii.gz), pulls out the middle timepoint and calls it > template.nii.gz, bbregisters func to anat and creates a > register.dof6.lta file in each of the functional run folders, > transforms the aparc+aseg from the subject's mri folder and > binarizes it into a brainmask (brain.nii.gz), and runs mc-afni > using f.nii.gz as the input vol and template.nii.gz as the > template vol to create the motion corrected volume (fmcpr.nii.gz). > Is this correct? > > yes > > Then when I run selxavg3-sess it somehow mri_converts an > intermediary motion corrected volume from the mc-afni command > above (eg <run#>/tmp.mc-afni2.20097/outvol.nii.gz) into an > fmc.nii.gz file in each run folder. Are these fmc.nii.gz's > supposed to be coregistered between runs? (i.e. if the subject > moved a bunch between two of the runs, would those two volumes be > aligned at all?). How do these files work? > > Not with -per-run. per-run was designed with the idea that you would > beresampling to some common space (eg, surface or mni305 or cvs), and > then running sexlavg3-sess on that data. If you want all the > fmc.nii.gz to be in the same space, then use -per-session. > > At the end I have an analysis directory with my betas, sigmaps, > etc. What functional volume is everything registered to? Is the > transform between this functional volume and anatomical space the > register.dof6.lta file located in the session directory? > > Thanks for bearing with me! > -David > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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/

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Bug Reporting: recon-all -s 001 exited with ERRORS
by Rosalia Dacosta Aguayo 13 Nov '17

13 Nov '17

Hello FreeSurfer Developers, I am attempting to compute autorecon1 in a subject to see how it works recon-all in a stepwise as described in the tutorial. Sorry if this is a very naive question but it is the first time I am trying to run an analysis with FreeSurfer. After running: *r* *econ-all -subjid 001 -autorecon1 -i S_001.nii.gz* I have found that it crashes with the following warning: *recon-all -s 001 exited with ERRORS at dom * I have seen that the problem comes from orig_nu.log Does anyone have any thoughts on how to trouble-shoot this problem? I have attached the recon-all.log and the orig_nu.log in case it is of any use. Kind regards, Rosalia

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[FSL] Tenure-Track Research Fellowships in Precision Imaging - University of Nottingham (fwd)
by Bruce Fischl 13 Nov '17

13 Nov '17

FYI ---------- Forwarded message ---------- Date: Mon, 13 Nov 2017 10:59:30 +0000 From: Stamatios Sotiropoulos <stamatios.sotiropoulos(a)NDCN.OX.AC.UK> Reply-To: FSL - FMRIB's Software Library <FSL(a)jiscmail.ac.uk> To: FSL(a)jiscmail.ac.uk Subject: [FSL] Tenure-Track Research Fellowships in Precision Imaging - University of Nottingham Dear All A number of unique opportunities are available for Tenure-track Research Fellowships in the University of Nottingham in the field of Precision Imaging. Potential topics include Neuroimaging-based disease biotyping, Imaging-based neuromodulation, and MR Spectroscopy. More details can be found online: http://www.nottingham.ac.uk/research/researchwithus/fellowships/beacon-fell owships.aspx The deadline for applications is Monday 4 December 2017. Best wishes Stam ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Stamatios N Sotiropoulos, PhD *Associate Professor Sir Peter Mansfield Imaging Centre School of Medicine, Queens Medical Centre The University of Nottingham, NG72UH *Honorary Research Fellow Centre for Functional MRI of the Brain (FMRIB) University of Oxford t: 0115 82 31027 w: www.nottingham.ac.uk/medicine/people/stamatios.sotiropoulos ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Re: [Freesurfer] Fw: Multiple comparison, color maps and contrast
by Douglas N Greve 13 Nov '17

13 Nov '17

can you send pics of the two patterns? Also, please remember to post to the list! doug On 11/10/2017 06:16 PM, Fabrizio Pizzagalli wrote: > Hi Douglas, > > I am not obtaining the same pattern testing for Group A > Group B > (c=[1 -1]) and Group A < Group B (c=[-1 1]). > That's why I am a bit confused. > > Thank you very much! > fab > > On Fri, Nov 10, 2017 at 12:29 PM, Douglas Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > the sig is signed by the sign of the contrast so that you can see > both sides. The p-values is two-sided > > > > On 11/10/17 3:25 PM, Fabrizio Pizzagali wrote: > > Hello, > When comparing 2 groups I obtain negative sig.mgh values > testing for Group A > Group B. > Shouldn't I get positive values of sig.mgh when testing for > Group A < Group B? > > Thank you. > Best, > fab > > > > > > 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> . 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. > > -- 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/

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7 T analysis - does GPU help?
by Melanie Ganz 13 Nov '17

13 Nov '17

Dear list, especially Bruce and Jon, We are starting to acquire images on the local 7T Philips scanner and would like to run them through FS. We did some pilot runs following what's described on http://surfer.nmr.mgh.harvard.edu/fswiki/SubmillimeterRecon and in http://www.sciencedirect.com/science/article/pii/S105381191730808X. That took approximately 42 hours. It looked reasonable but I estimate from the pilot run that some manual edits will be in order. This is quite tedious to do if the turnaround time is 2 days and we are looking at quite a few number of patients we want to run. Would we actually get any speedup if we utilize the -use-gpu flag (we don't have access to a gpu yet, but are getting one soon). I looked at the speedup factors and especially mris-inflate doesn't speed up too much (https://surfer.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide) . Kind regards, Mel

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"Halo" of low values around pial surface in Apparent Diffusion Coefficient maps from DWI registered to CVS template
by Mehta, Chintan 13 Nov '17

13 Nov '17

Dear FreeSurfer users, I'm using FS 6.0. I registered DWI scans to the CVS registrations of T1-weighted MRI scans as described at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0. The average diffusion coefficient (ADC) maps registered to CVS have a "halo" of very low values around the brain (right outside the pial surface of the cortex), which diverges from the expectation that ADC be lowest in white matter. See attached image of ADC in CVS space for one sample: adc-ANAT+CVS-to-avg35.png On the other hand, this halo of low values is not as apparent in the ADC maps in diffusion space (masked to voxels in subject's aseg in diffusion space): See attached image of ADC in diffusion space: diffusionSpace-adc.png For comparison, also attached are the subject's T1-weighted images registered to CVS space (final_CVSmorphed_tocvs_avg35_norm.png) and to diffusion space (diffusionSpace-brainmask.png) that underlay these spatial maps. On the other hand, fractional anisotropy (FA) maps in either CVS space or diffusion space look reasonable --- with FA highest along white matter fiber tracts. See attached screenshots for FA in CVS space (fa-ANAT+CVS-to-avg35.png) and FA in Diffusion space (fa-diffusionSpace.png; masked to aseg in diffusion space). This phenomena is typical across all samples. Is the halo of very low values surrounding the brain, adjacent to cortical gray matter, typical in ADC spatial maps registered to CVS? If so, is there a way to remove this halo of low values for ADC maps in CVS space? For example, the depth of this halo decreases when masking the ADC maps with the aseg.mgz for the CVS average template. The halo decreases furthermore when masking by the subject-specific aseg registered to CVS generated by mri_cvs_register ("final_CVSmorphed_tocvs_avg35_aseg.mgz"). In either case, the halo does not disappear. I'm concerned that these ADC mis-measurement e boundary may yield significant issues in GLM analysis. If there is no way to remove this halo, is a GLM of ADC maps in CVS space more reliable for voxels masked to white matter? Thank you. Best, Chintan

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TRACULA
by 郑凤莲 13 Nov '17

13 Nov '17

Hi Professor, Thank you for looking at my e-mail in your busy time. I am a student studying TRACULA in Freesurfer. But I got into troubles in my study. Could you help me resolve some problems? 1. When I do the first step, after the ‘bbregister done’, it say 'with errors', as the following picture. Do you know what it means? How to solve it? 2. In another computer, I finished the first step with out errors. But in the second errors, I met a trouble again. Does it because of the version of Freesurfer? I really need your help. If I don't describe my problem clearly, please contact me at any time. I am looking forward to your reply. Thank you very much. Sincerely, Zheng

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Re: [Freesurfer] Adding control points to aparc+aseg
by Nicholas Goh 13 Nov '17

13 Nov '17

I have still been having trouble with fixing the white matter of the aparc+aseg.mgz file for a subject. I have tried using recon-all -autorecon2-cp -autorecon3 -subjid XXXX recon-all -autorecon2-wm -subjid XXXX recon-all -autorecon2-wm -autorecon3 -subjid XXXX None of these have solved the issue, and I was hoping for help in finding a way to fix this? There are other more extreme examples, but this one seems to have an error at [-7, 114, 133] Thank you for the help, Nicholas Goh On Thu, Sep 28, 2017 at 5:34 PM, Nicholas Goh <ngoh95(a)gmail.com> wrote: > Ping, is this okay to do? I Think it is but wanted to check before sending > ---------- Forwarded message ---------- > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Date: Thu, Sep 28, 2017 at 5:23 PM > Subject: Re: [Freesurfer] Adding control points to aparc+aseg > To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> > > > Hi Nicholas > > why don't you tar, gzip and upload your subject and we will take a look. > Make sure to tell us the coordinates of where you are trying to fix things > > cheers > Bruce > > > On Thu, 28 Sep 2017, Nicholas Goh wrote: > > I am still having trouble with getting the aparc+aseg to recognize sections >> that should be white matter as such. Using the control points paired >> withrecon-all -autorecon2-cp -autorecon3 -subjid XXXX >> >> did not work, after 4 or 5 attempts with different control points, and >> using >> recon-all -autorecon2-wm -s XXXX >> also did not yield appreciable results. Is there anything else that I >> might >> be able to try to fix this? >> Thank you for all the help, >> >> Nicholas Goh >> >> On Wed, Sep 27, 2017 at 12:49 PM, Elijah Mak <fkm24(a)medschl.cam.ac.uk> >> wrote: >> Hi Nicholas, >> >> In such situations, I have learned that autorecon2-wm after adding WM >> voxels seems to work pretty well. Hope that helps. >> >> Best Wishes, >> Elijah >> >> On 27 September 2017 at 16:46:43, Nicholas Goh (ngoh95(a)gmail.com) >> wrote: >> >> Bruce, >> Thank you for the response. Attempting to use this method has >> not produced results, and I am unsure how to proceed or if I had >> performed it improperly. I have attached an example of the >> control points being placed, if that helps any. >> Thank you, >> >> Nicholas Goh >> >> On Wed, Sep 27, 2017 at 11:04 AM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >> Hi Nicholas >> >> yes, possibly, depending on why you are missing >> chunks. If the white matter in the regions you are >> missing has intensity values significantly < 110 >> then what you are doing should help. The control.dat >> file must be place in the subject/tmp dir for us to >> find it. >> >> cheers >> Bruce >> On Wed, 27 Sep 2017, Nicholas Goh wrote: >> >> I am attempting to fix the >> aparc+aseg.mgz file for an image, and >> wanted to check to see if I am >> doing it correctly.What I was doing >> which seemed to be ineffective was >> 1)create a new point set of control >> points labelled control.dat >> 2)place control points along what should >> be white matter >> 3)save point set >> 4)run recon-all -autorecon2-cp >> -autorecon3 -subjid XXXX >> >> Is this the correct way to go about >> fixing aparc+aseg files that are missing >> chunks of the brain? Is >> there a better way to go about this? >> Thanks for the help, >> >> Nicholas Goh >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> 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 . 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://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 . 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://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 . 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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