Freesurfer

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beta testing FreeSurfer v7 beta: recon-all-status.log, samseg
by Antonin Skoch 28 Feb '20

28 Feb '20

External Email - Use Caution Dear experts, I began to test beta v7 version of FreeSurfer. I noticed that some entries in recon-all-status.log seem missing (i.e. white and pial surface placement - there is entry Cortical Parc while following entry is Refine Pial Surfs). Running samseg` --t1w $s/mri/T1.mgz --t2w $s/mri/T2.mgz --s $s --refmode t1w exits with error in samseg2recon since command set segvol = `find "$samsegdir" -iname "*crispSegmentation.nii" -print` results with empty string set to segvol variable. Antonin

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Re: [Freesurfer] DOSS questions
by Ferraro, Pilar 28 Feb '20

28 Feb '20

External Email - Use Caution Thank you so much for all the help! Below you can find few remaining questions I have following your suggestions! Message: 6 Date: Mon, 24 Feb 2020 09:24:00 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] GLM DOSS questions To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <62cf0ae8-3d78-aa44-7a44-17cd603a8934(a)mgh.harvard.edu<mailto:62cf0ae8-3d78-aa44-7a44-17cd603a8934@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" On 2/21/2020 4:01 AM, Ferraro, Pilar wrote: ????????External Email - Use Caution Dear Freesurfer experts, I?ve just completed a GLM analysis in Freesurfer and I?d like to be sure that all the steps I?ve performed are the right ones. My analysis is looking at age related changes in cortical thickness in one group of patients, after regressing out the effects of disease duration. I obviously assume an inverse relationship between age and cortical thickness so that older age would be associated with cortical thickness reductions in specific brain regions. To test this hypothesis with Freesurfer I?ve used a GLM DOSS design. I?ve generated a fsgd file with the first column being the list of patients, the second column the age of patients, and the third column the disease duration. Then I?ve run the mris_preproc command. Afterward,? I?ve generated 2 contrast matrices (one for the left and one for the right hemisphere) with the following structure: 0 -1 0. 1 question. Is the contrast matrices structure I?ve chosen the most appropriate one for the hypothesis I?d like to test? Yes, but if you are going to use -1, you need to keep track of that when you specify the sign (but you are using abs so it does not matter). Also, you don't need different fsgd and contrast files for each hemisphere. >> Thank you! Then, I?ve run the glm analysis using the mri_glmfit command. To visualize the results I?ve used the freeview -f command and set the overlay_threshold to 1,5 instead of 4, cause I was interested in looking at all results significant at p < 0.05. 2 question. Is the overlay_threshold I?ve used the correct one? for visualization, you can use whatever threshold you want. But if you are going to use monte carlo simulations, then you need p<.001. If you want to keep p<.05, then you have to do permutation. >> I totally understand your point on the need for p<.001 threshold for Monte Carlo Simulation. However, in this first step of results visualization as an exploratory starting point I was just interested in uncorrected results generated with the mri_glmfit command with threshold p<0.05. So, was the command I’ve reported above the correct one in this case? Lastly, I was interested in looking at my results after Montecarlo correction, so I?ve run the simulation using the mri_glmfit-sim command. However, here I?ve changed few options: mri_glmfit-sim \ ? --glmdir lh.dur.glmdir \ ? --cache 4 neg \ (here I?ve changed to 1,5 since I was interested again at a P value < 0,05 and not < 0.0001 and I?ve changed the neg option with abs since I was interested in absolute values identified through the previously run analysis) ? --cwp? 0.05\ ? --2spaces 3 question. Are the edits I made to the command correct? It is not perfectly clear to me which one should be the preferred sign for the analysis (neg, pos or abs?). abs is an unsigned test. If you have an aprior hypothesis, then you can set the sign to that. Eg, if you are expecting the age slope to be negative, then you could choose negative (or in your case positive since you flipped the sign in the contrast) >> Sounds good, thanks for the explanation! In the end, in order to visualize the Montecarlo corrected results I?ve used again the Freeview -f command and again I?ve sent the overlay threshold to 1,5 since I was interested in all significant clusters at P < 0,05. 4 question. Again, this threshold is the correct one for my purpose? It will show all the clusters that are at p<.05 corrected. >> Ok, so, if I’ve correctly understood, I need to change this step either: a) Running a permutation instead of Monte Carlo simulation if I want to keep the p value < 0.05, or b) keep the Monte Carlo Simulation but change the p value to < 0.001. Is that correct? Also, for the Permutation analysis should I follow your detailed steps explanation reported in here: MultipleComparisonsV6.0Perm<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.…> ? I have one last question concerning the Montecarlo simulation. Are there any cases in which you would suggest to do not use it since it would not be an appropriate correction? I'm recommending that everyone use permutation at this point. MC can generate inlfated false positives >> Thanks for the helpful tip! I’m a little bit concerned cause I have a quite small sample size (26 patients and 37 healthy controls for the comparison, while the regression analysis is run only in the patients group). At this point I presume it would be better to firstly run the permutation with p< 0.05, and then, only in case of no results with this procedure, eventually look at results with Monte Carlo p<0.001. Would that be a good option? Thanks again for all your help! Sorry for the long email but I needed to report all the steps in order to get an answer. Many thanks for all the help you?ll be able to provide. Best, Pilar Ferraro _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/0… ------------------------------ Message: 7 Date: Mon, 24 Feb 2020 09:25:38 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] surfreg function To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <6075b7ad-ad3a-c483-2208-ee6fd048f5d0(a)mgh.harvard.edu<mailto:6075b7ad-ad3a-c483-2208-ee6fd048f5d0@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" it is ok to spec -surfreg, but is not necessary in this case mris_preproc will change the name when you spec a target subject (eventhough the says that the default is sphere.reg) On 2/21/2020 6:20 AM, Marina Fern?ndez wrote: ????????External Email - Use Caution Hi Doug, Thank you for your replay. I understood that if I did not specify "--surfreg my_avg_subject.sphere.reg" ?mri_preproc was going to use the original file (sphere.reg), because in the help of mri_preproc it mentions this: --surfreg SurfReg : default is sphere.reg With this in mind,do you think it would not be necessary to specify it in mris_preproc? What is the difference between sphere.reg and my_avg_subject.sphere.reg? Best wishes, Marina _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/8… ------------------------------ Message: 8 Date: Mon, 24 Feb 2020 09:26:14 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <362fe77d-51d2-2e69-1e5d-e273321b0dde(a)mgh.harvard.edu<mailto:362fe77d-51d2-2e69-1e5d-e273321b0dde@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Not sure what you are trying to do. An lta file is a matrix and nifti is a format for storing images. On 2/21/2020 7:52 AM, Kate Marvel wrote: ????????External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/e… ------------------------------ Message: 9 Date: Mon, 24 Feb 2020 09:31:30 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] Optseq2 help needed To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <c4cecc27-ad82-b2bb-b174-0a6a9b20490e(a)mgh.harvard.edu<mailto:c4cecc27-ad82-b2bb-b174-0a6a9b20490e@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" By default, optseq2 assumes that you want to perform an FIR analysis where you get an average for each post-stimulus time point so that you can create a waveform. This is in contrast to assuming the shape to the hemodyn respnse where you only estimate a single value (the amplitude). By default, the time between FIR waveform points is the TR, but you can perform sub-TR estimation by setting the dPSD to less than the TR. The problem is that every estimate you make reduces the efficienecy. So, assuming a shape is more efficient than an FIR because it only has one estimate. An FIR with dPDS=TR is more efficient than dPSD=TR/2 because there are half as many estimates. Probably when you go to analyze the data you will use an assumed shape, and then you will get the efficiency back. On 2/21/2020 9:43 AM, Gergely Darnai wrote: ????????External Email - Use Caution Dear Developers, I am planning to run PVT (psychomotor vigilance task) in fMRI using event related design. This is an extremely simple reaction time task: participant has to respond to the appeared geometric shape as quickly as possible. The key feature of this paradigm is that we will have fluctuating and quite rapid event presentation times (ranging between 300 and 500 msec). Another important information is that we will use FSL FEAT for the evaluation. We decided to use opseq2 to optimize the design with the following parameters: optseq2 --ntp 150 --tr 2 --psdwin 0 20 --ev evt1 1 45 --nkeep 3 --o exp --nsearch 10000 --tnullmin 3 --tnullmax 11 --repvar 10 Although with this design I get quite satisfying efficiency and VRF scores I do not understand that if I decrease dPSD why does it have significant negative effect on efficiency and VRF. Could you explain this? If I understand well, this is the only option to shift the onset of the event from the scanning points, and I would assume that if there is fluctuation in time between scanning points and stimuli presentation, it would help to "catch" the hemodynamic response easier (if the stimulus onset always goes together with the scans, we can always catch the same timepoints of the HRF). Did I misunderstand something? If I use FSL that is based on HRF estimation (and not on FIR), do these parameters (dPSD) and scores (efficiency & VRF) have meaning and function at all? My last question is related to event duration. Although I have fluctuating and short events, as you can see I chose 1 sec (because it has to be the integer multiple of the dPSD). Is it problematic? Thank you for your suggestions, Gergely ----------------------------------------- Gergely Darnai PhD Department of Behavioural Sciences Medical School, University of P?cs Phone: +36/72/536-256 Fax: +36/72/536-257 H-7624 Szigeti u. 12, P?cs, Hungary _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/a… ------------------------------ Message: 10 Date: Mon, 24 Feb 2020 09:33:41 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] Creating the pial surface of the cerebellum: how to let the mris_make_surfaces to push the pial surface to the boundary To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <04884b22-53f5-2c7a-e07b-0aa0209532e6(a)mgh.harvard.edu<mailto:04884b22-53f5-2c7a-e07b-0aa0209532e6@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Try setting -max XXX where XXX is the maximum allowable thickness. It is default to 5, so try something large On 2/21/2020 11:36 AM, CiRong Liu wrote: ????????External Email - Use Caution Dear experts of the freesurfer, I was trying to create the white matter and pial surfaces of the?cerebellum of the marmoset, based on ultra-high (80um) resolution ex-vivo images. I manually segment the cerebellum into the white matter and the gray matter and change the header information to 1mm. Based on the manual?segmented files, I created white matter surfaces (rh.orig). I tried to use the mris_make_surfaces to expand the white matter to create the matched pial surface. However, the /mris_make_surfaces/ failed to push the surface enough. See the attached files and screenshots. I tried smoothing the segmentation, enhancing the contrasts, and tested different expert option (for example: -max_csf 0.1 -min_gray_at_csf_border 1) This was this best I got, but still cannot get an optimal result (not pushed enough): /mris_mask_surfaces -max_csf 0.1 -min_gray_at_csf_border 1 -orig_wm orig -orig_pial orig -noaseg -noaparc -T1 ceb_sm marmosetceb rh / Since I have already manually segmented the cerebellum, *is there a way to force the /mris_make_surfaces/ to expand to the boundary of the image?* The files can be download to replicate what I did: https://pitt.box.com/s/6269a9mnwbs6zi0azn08dn55u47yfa7i Thank you very much! Best Regards, CiRong Liu _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/b… ------------------------------ Message: 11 Date: Mon, 24 Feb 2020 09:36:58 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] Version Beta 7.0 To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <51a3e156-250a-4679-07e4-c2deaebbb7be(a)mgh.harvard.edu<mailto:51a3e156-250a-4679-07e4-c2deaebbb7be@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" We have not released stable 7 yet. Technically we have not released 7beta yet but only because I need to make the announcement and write up some docs. On 2/24/2020 2:46 AM, Victor Montal Blancafort wrote: ????????External Email - Use Caution Freesurfer developers, I have seen from the download webpage, that there is already a v7.0 beta version. Since we were planing to re-run a lot of individuals 1000+ with Freesurfer6, I was wondering if you could provide timings regarding the release of stabe 7.0. Also, could you briefly explain the main changes in this version? We are mainly interested on cortical thickness analysis, so... there will be big differences in the recon-all pipeline? Thank you in advance! V. _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/9… ------------------------------ Message: 12 Date: Mon, 24 Feb 2020 09:41:09 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Subject: Re: [Freesurfer] cluster size threshold To: <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <b66960f1-e9c7-4ccf-86db-4c6444bfbca2(a)mgh.harvard.edu<mailto:b66960f1-e9c7-4ccf-86db-4c6444bfbca2@mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" You need to find the correct CDF file, eg, if the final FWHM is 12, it would be in $FREESURFER_HOME/average/mult-comp-cor/fsaverage/lh/cortex/fwhm12/abs/th30/mc-z.cdf To get the FWHM look in glmdir/fwhm.dat and round down in the mc-z.cdf file, find the row where the MaxClustCDF drops below .05/2=.025, then look at the MaxClustBin for the critical cluster size On 2/24/2020 6:49 AM, Elisa Castaldi wrote: ????????External Email - Use Caution Dear experts, To perform a Monte Carlo based cluster correction, I have run the following line: mri_glmfit-sim --glmdir glmdir --mczsim 3 abs --cwp 0.05 --2spaces --a2009s I need to figure out which is the minimum number of voxels required for a cluster to be considered significant. In other words, which is the cluster _size_ threshold in this case? Where can I find this information? Thanks Elisa _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/d… ------------------------------ Message: 13 Date: Mon, 24 Feb 2020 08:47:49 -0600 From: Kate Marvel <kmarvel54(a)gmail.com<mailto:kmarvel54@gmail.com>> Subject: Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <CAG9yhu5o0ehKA-2oLLovmUFC2M1SrPowGioDiesR2Dsbna4N3A(a)mail.gmail.com<mailto:CAG9yhu5o0ehKA-2oLLovmUFC2M1SrPowGioDiesR2Dsbna4N3A@mail.gmail.com>> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Douglas, Is there a way to save the registered PET image in NIfTi format instead of .lta? Kate On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> wrote: Not sure what you are trying to do. An lta file is a matrix and nifti is a format for storing images. On 2/21/2020 7:52 AM, Kate Marvel wrote: External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, _______________________________________________ Freesurfer mailing listFreesurfer(a)nmr.mgh.harvard.eduhttps<mailto:listFreesurfer@nmr.mgh.harvard.eduhttps>://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 -- kate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/f… ------------------------------ Message: 14 Date: Mon, 24 Feb 2020 09:50:25 -0500 (EST) From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <alpine.LRH.2.21.2002240949160.22762(a)door.nmr.mgh.harvard.edu<mailto:alpine.LRH.2.21.2002240949160.22762@door.nmr.mgh.harvard.edu>> Content-Type: text/plain; charset="utf-8" Hi Kate the .lta format is for a linear registration (in ascii). YOu can just cat it to see the contents - it is not a PET image (which will be stored in .mgz or .nii). mri_convert or mri_vol2vol can be used to apply the registration and/or change the output format (if you specify file.nii or file.nii.gz it will write in Nifti) cheers Bruce On Mon, 24 Feb 2020, Kate Marvel wrote: ????????External Email - Use Caution???????? Hi Douglas, Is there a way to save the registered PET image in NIfTi format instead of .lta? Kate On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> wrote: Not sure what you are trying to do. An lta file is a matrix and nifti is a format for storing images. On 2/21/2020 7:52 AM, Kate Marvel wrote: ????????External Email - Use Caution???????? Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- kate ------------------------------ Message: 15 Date: Mon, 24 Feb 2020 14:50:05 +0000 From: Adam Rytina <adam.rytina(a)outlook.cz<mailto:adam.rytina@outlook.cz>> Subject: Re: [Freesurfer] Apply transformation To: "Greve, Douglas N.,Ph.D." <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>>, "freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>" <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>>, "freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Message-ID: <AM0PR0602MB3377640CAED11562C48DB7349AEC0(a)AM0PR0602MB3377.eurprd06.prod.outlook.com<mailto:AM0PR0602MB3377640CAED11562C48DB7349AEC0@AM0PR0602MB3377.eurprd06.prod.outlook.com>> Content-Type: text/plain; charset="iso-8859-2" External Email - Use Caution Hello all, is it possible to transform a binary mask (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) and change a final FOV by specifying a diffusion reference image? Or the transform can be applied only on structural image? I am still struggling with the transformation of my binary mask as explained below. Thanks a lot Regards Adam ________________________________ Od: Adam Rytina <adam.rytina(a)outlook.cz<mailto:adam.rytina@outlook.cz>> Odesl?no: st?eda 19. ?nora 2020 8:11 Komu: Greve, Douglas N.,Ph.D. <DGREVE(a)mgh.harvard.edu<mailto:DGREVE@mgh.harvard.edu>> P?edm?t: Fw: [Freesurfer] Apply transformation Hello, please, could you help me with this case? What am I doing wrong? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> za u?ivatele Adam Rytina <adam.rytina(a)outlook.cz<mailto:adam.rytina@outlook.cz>> Odesl?no: sobota 15. ?nora 2020 19:52 Komu: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> P?edm?t: Re: [Freesurfer] Apply transformation External Email - Use Caution Thanks, unfortunately, I am making some mistake but I don?t know where. First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical). Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here. Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space. In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg" To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image. The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii. Please, do you know where I make mistake? Thanks a lot ________________________________ Od: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> za u?ivatele Douglas Greve <dgreve(a)mgh.harvard.edu<mailto:dgreve@mgh.harvard.edu>> Odesl?no: sobota 15. ?nora 2020 17:15 Komu: freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> P?edm?t: Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam _______________________________________________ Freesurfer mailing list Freesurfer(a)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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/7… ------------------------------ Message: 16 Date: Mon, 24 Feb 2020 15:54:49 +0100 From: Marina Fern?ndez <marina.fdez.alvarez(a)gmail.com> Subject: [Freesurfer] skull stripping problem To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAALjZmedHxapja0jycg2bF=JC81kOCqHytmcnM2ziwrX2T_gUA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 And the problem was solved in the brainmask.mgz volume because I can see the temporal lobe completely, but the surfaces are still displaced. In order to correct the surfaces I used the white matter edit tool but there is no change after correcting WM and running the recon-all -autorecon2-wm -autorecon3. I also used control points and but the following error was shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I detected that there are very high values in the white matter of this part of the temporal lobe (even 132), maybe it has something to do. What can I do to solve the problem with this subject? Thank you very much in advance. Best regards, Marina. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/a… ------------------------------ Message: 17 Date: Mon, 24 Feb 2020 09:04:52 -0600 From: Kate Marvel <kmarvel54(a)gmail.com> Subject: Re: [Freesurfer] how to convert the registered file (.lta) into NIfTI format in PETsurfer To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <CAG9yhu7rcBLfPeMo-L9p7iaN7O54Gjm2PB9tJjMtDvSH-Q4kqw(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi Bruce, Thank you very much Bruce. Kate On Mon, Feb 24, 2020 at 8:50 AM Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Kate the .lta format is for a linear registration (in ascii). YOu can just cat it to see the contents - it is not a PET image (which will be stored in .mgz or .nii). mri_convert or mri_vol2vol can be used to apply the registration and/or change the output format (if you specify file.nii or file.nii.gz it will write in Nifti) cheers Bruce On Mon, 24 Feb 2020, Kate Marvel wrote: External Email - Use Caution Hi Douglas, Is there a way to save the registered PET image in NIfTi format instead of .lta? Kate On Mon, Feb 24, 2020 at 8:26 AM Douglas N. Greve <dgreve(a)mgh.harvard.edu wrote: Not sure what you are trying to do. An lta file is a matrix and nifti is a format for storing images. On 2/21/2020 7:52 AM, Kate Marvel wrote: External Email - Use Caution Hi All, How do you convert the registered file (.lta) into NIfTI format in PETsurfer. Thanks, _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- kate _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- kate -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/8… ------------------------------ Message: 18 Date: Mon, 24 Feb 2020 15:50:26 +0000 From: "Russo, Andrew William" <AWRUSSO(a)mgh.harvard.edu> Subject: [Freesurfer] samseg permissions error To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <BL0PR04MB4593810C0E71B357FAEF1011E8120(a)BL0PR04MB4593.namprd04.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-1" Hello Freesurfer Developers, I am trying to use the "samseg" function in /usr/local/freesurfer/dev but do not have permission to access the directory /usr/local/freesurfer/dev/subjects/fsaverage. Is this a restricted directory? ValueError: file /usr/local/freesurfer/dev/subjects/fsaverage/mri/orig.mgz does not exist ERROR: fs_time run_samseg I did not find any related issues with samseg on the archive and I have had it work in the past. Before running samseg I sourced the freesurfer environment: export FREESURFER_HOME=/usr/local/freesurfer/dev source $FREESURFER_HOME/SetUpFreeSurfer.sh (Using Freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) Thank you in advance, Andrew ____________ Andrew Russo Clinical Research Coordinator Multiple Sclerosis Imaging Lab Massachusetts General Hospital 149 13th Street | Boston, MA 02129 617-726-7531 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/9… ------------------------------ Message: 19 Date: Mon, 24 Feb 2020 16:15:20 +0000 From: "Harrigan, Timothy P." <Timothy.Harrigan(a)jhuapl.edu> Subject: [Freesurfer] Registration error To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <1fb1864f806f4eb89ba47f72b3d2a4be(a)aplex11.dom1.jhuapl.edu> Content-Type: text/plain; charset="us-ascii" External Email - Use Caution Hi, I'm trying to learn to use Freesurfer to see if I can use it for some academic work on TBI. I downloaded it to a spare laptop at home, and filled out the registration form, and I got a message that stated "Registration Error: Spammer. Go Away." How could I address this? Thanks Tim Timothy P. Harrigan ScD Research and Exploratory Development Division Johns Hopkins University Applied Physics Laboratory Phone: 240-228-5943 Cell/Text: 240-280-9444 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200224/c… ------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 192, Issue 32 *******************************************

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Re: [Freesurfer] Registration error
by Hoopes, Andrew 28 Feb '20

28 Feb '20

Hi Tim, Did you use an auto-completion plugin to fill out the webform? If so, can you disable it and try again? We have a fairly ~old-fashioned~ spam detector that checks for completed entries in hidden fields. best, Andrew From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Harrigan, Timothy P." <Timothy.Harrigan(a)jhuapl.edu> Reply-To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Date: Monday, February 24, 2020 at 11:16 AM To: FS Help <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Registration error External Email - Use Caution Hi, I’m trying to learn to use Freesurfer to see if I can use it for some academic work on TBI. I downloaded it to a spare laptop at home, and filled out the registration form, and I got a message that stated “Registration Error: Spammer. Go Away.” How could I address this? Thanks Tim Timothy P. Harrigan ScD Research and Exploratory Development Division Johns Hopkins University Applied Physics Laboratory Phone: 240-228-5943 Cell/Text: 240-280-9444

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MNI coordinates from Thalamic nuclei
by Corinna Bauer 28 Feb '20

28 Feb '20

External Email - Use Caution Hi all, Is there a way to obtain the MNI coordinates for the thalamic nuclei? Thanks Corinna

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OHBM Brainhack 2020
by Remi gau 28 Feb '20

28 Feb '20

External Email - Use Caution Hello all, The OHBM Open Science Special Interest Group<https://ossig.netlify.com/> is very happy to announce that the 8th Annual OHBM Brainhack will be held June 23-25 at Phi Centre in Montreal. A hackathon? For who? At the OHBM Brainhack, members of the community gather to work collaboratively on common projects. This year we would like to especially welcome new attendees who have never been to hackathon before. We will provide TrainTrack sessions tailored for beginners and opportunities to directly apply new skills by joining a hackathon project. All members of the community are invited to take part in the OHBM Brainhack 2020! Applications are now open for the OHBM Hackathon Travel Awards. The Open Science Special Interest Group is pleased to offer 20 travel awards that will include free registration at the hackathon plus $500 USD that will go towards covering part of the expenses incurred to attend the hackathon. Submit your application no later than March 15th: http://ossig.netlify.com/awards. Registration for the OHBM Brainhack will open in the middle of March. Soon after OHBM abstract acceptances are sent out, registration for the OHBM Brainhack will open. In the past two years the hackathon was fully booked, and we therefore recommend to register early. Seats will be allocated on a first come first serve basis. In an effort to increase diversity at the event, we will reserve part of the seats to attendees who attend a hackathon for the first time or who come from traditionally under-represented groups in science or in past hackathons. Please contribute your favorite TrainTrack session! Are there specific topics that you would like to see covered in the Hackathon training sessions? Please let us know using this form<https://forms.gle/LbngA8xVDYj3Ep9W7>. We are very excited to welcome you to the OHBM Hackathon! For most recent updates please see the OS SIG website<http://ossig.netlify.com/>, follow us on twitter @OHBMopen<https://twitter.com/ohbmopen> and follow the hbm-hackathon channel on the brainhack mattermost<https://mattermost.brainhack.org/signup_user_complete/?id=orpd9qqjb7gqpnwg5…>. Remi Gau, Elizabeth Levitis and Camille Maumet for the OHBM Open Science Special Interest Group

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seg.mgz testing for FS7 beta
by Zeng, Victor (BIDMC - Keshavan - Psychiatry) 27 Feb '20

27 Feb '20

Hi Freesurfer team, I've run samseg for one participant, using the /mri/T1.mgz as the input, but the output seg.mgz is awful, w/ the ventricles being overestimated and the outer perimeter of the gray matter considered as the "Head-ExtraCerebral." I know in mind you all just want to know if it runs in FS7.0beta, but is this something I'm suppose to be expecting? best, Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.

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Re: [Freesurfer] aparcstats2table
by Devika K 27 Feb '20

27 Feb '20

External Email - Use Caution Hi, Can I use the below command to extract the cortical thickness using Destrieux Atlas from longitudinally preprocessed subjects? aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas thickness \ --parc aparc.a2009s \ --tablefile lh.aparc.a2009.thickness.table Regards Devika K

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Job post: full-time research assistant in the lab of Dr. Emily Finn, Dartmouth College
by Emily S. Finn 27 Feb '20

27 Feb '20

External Email - Use Caution Dear Freesurfer users, The laboratory of Dr. Emily Finn in the Department of Psychological and Brain Sciences at Dartmouth College is seeking a full-time Research Assistant for a targeted start date of July 2020. The research of the lab focuses on individual differences in brain activity and connectivity, and how these relate to behavior. Some key questions are: How do our intrinsic traits bias our perceptions and judgments, and how is this reflected in patterns of brain activity? Why might different people arrive at different interpretations of the same experience? Our research combines behavioral, neuroimaging and computational modeling techniques to study individual differences in cognition, especially under rich, dynamic, “naturalistic” stimulation such as watching movies or listening to stories. This position is especially well-suited for individuals planning to apply for a PhD in cognitive neuroscience or psychology. The position would be for an initial 1 year, with an ability to renew up to 2 additional years thereafter based on performance. Preference will be given to applicants who are willing to stay at least two years. Questions may be directed to Emily Finn (emily.s.finn(a)dartmouth.edu) For full consideration, please apply by March 13, 2020. Position Purpose Plays a crucial role in helping to set up the lab as well as conduct experiments. The Research Assistant’s role will involve administrative tasks, such as purchases, participant recruitment, ethics applications, organizing files, and setting up meetings. Conducts research, including designing experiments, collecting data, analyzing data, and writing papers, with the aim of completing an independent research project by the end of their time. The Research Assistant will learn techniques in programming, functional MRI brain scanning, and in-person and online behavioral experimentation. Required Qualifications - Bachelor’s degree with a major in psychology, neuroscience, cognitive science, computer science, biology, or a similar field - Previous experience in one or more laboratory methods, procedures and techniques as well as the equipment and instruments, e.g., fMRI data acquisition, eye-tracking, behavioral experimentation - Ability to work independently and apply critical thinking and sound judgment - Excellent organizational and time management skills - Knowledge of software for writing and presentation (e.g., Microsoft Office), and online scientific literature search engines Preferred Qualifications - Two years of relevant laboratory/ research experience during undergraduate - General programming and computational skills for data analysis (e.g., Python, MATLAB, R) - Experience with neuroimaging analysis software (e.g., AFNI, SPM, FSL) and experiment creation (e.g., PsychoPy, Psychtoolbox) - Experience working with human participants For more information or to apply: https://searchjobs.dartmouth.edu/postings/53845 -- Emily S. Finn, PhD Assistant Professor, beginning July 2020 Psychological & Brain Sciences Dartmouth College esfinn.github.io<http://esfinn.github.io>

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Full analysis chain without Topology fix, Talairach check?
by HsuD3＠mskcc.org 27 Feb '20

27 Feb '20

External Email - Use Caution Dear Freesurfers, I am attempting to run the full reconstruction in Freesurfer on several hundred patient images with diseased areas of the brain. Without skipping any steps of the analysis chain, I am able to complete the full reconstruction for about 50% of said patients. When the analysis is able to complete, the disease sites are generally not included in the white or gray segmentation labels, which is ideal for my use case. However, when the disease is far from the cortical surface, it generally results in a large topological defect. (In other cases, the Talairach check fails.) I would like to know, does it really make sense to try to analyze the images with a "real" topological defect, and if so, how to accomplish it? I have tried to run the reconstruction with flags "-nofix" and "-notal-check" to accept an imperfect Talairach transform and avoid crashes trying to fix these unfixable topological defects. Unfortunately, the step "mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a file "surf/lh.orig.premesh" which is not found, causing a crash. From what I can understand, that file is produced by the so-called old topology fix [1], so it would imply that a full analysis chain is not supported if you eschew topology-fixing. Is this a feature, or do you recommend modifying the logic of the script to work around it? This is as far as I got, but I suppose there may be steps later in the analysis chain that will also look for files only produced if the topology fix runs. For your information, I am currently using the nightly build from February 12 for CentOS7, and I am amenable to switching to an older or newer build. Thank you for taking the time to help me. Best regards, Dylan Hsu, Ph.D Memorial Sloan-Kettering Cancer Center [1] <https://github.com/freesurfer/freesurfer/tree/dev/scripts#L3128-L3139> https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807349f… ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.

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Segmentation problem
by Marina Fernández 27 Feb '20

27 Feb '20

External Email - Use Caution Dear Freesurfeer experts, After running the recon-all, a part of the temporal lobe of one subject was removed. I used the watershed algorithm to be less agressive in the skull stripping step: recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 And the problem was solved in the brainmask.mgz volume because I can see the temporal lobe completely, but the surfaces are still displaced. In order to correct the surfaces I used the white matter edit tool but there is no change after correcting WM and running the recon-all -autorecon2-wm -autorecon3. I also used control points and but the following error was shown in the terminal when I run the recon-all -autorecon2-cp -autorecon3: recon-all -s sub_001 existed with errors I detected that there are very high values in the white matter of this part of the temporal lobe (even 132), maybe it has something to do. What can I do to solve the problem with this subject? Thank you very much in advance. Best regards, Marina.

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