Freesurfer February 2020

freesurfer@nmr.mgh.harvard.edu

96 participants
143 discussions

Apply transformation
by Adam Rytina 19 Feb '20

19 Feb '20

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

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surface analysis with RBV PET images
by Marina Fernández 18 Feb '20

18 Feb '20

External Email - Use Caution Hi experts, I would like to know how to work correctly on the surface with PET images to which the RBV method was applied. I have tried to do it using the mri_coreg and mri_gtmpvc function (applying as RBV method) to obtain the rbv.nii.gz volume. Then I have masked this volume with a GM cortical mask, and I have taken the output to the surface of the average subject of my dataset (which is in ico7) with the mri_vol2surf command. I have loaded the surface in the file inflated with tksurfer and there were too many holes (see attached image). Are these steps correct? What can I do so that there are not so many holes in the surface? *In each step I have been checking that the registration was correct. Thanks for your attention! Marina.

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help
by Parks, Sean 18 Feb '20

18 Feb '20

Hello, I am working through the tutorial fro FSFAST, and am up to the Preprocessing step. I followed the instructions as indicated and was not receiving errors up until the following command: preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run With this command I receive the error after the code runs for a while: MRISread(/home/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg): could not open file Reading target registration /home/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg No such file or directory ERROR: could not read /home/fsfast-tutorial.subjects/fsaverage/surf/lh.sphere.reg Checking the fsaverage/surf folder I do not see lh.sphere.reg or rh.sphere.reg. In the fsaverage/surf folder of my freesurfer home subjects, lh.sphere.reg and rh.sphere.reg are present. My question is: is rh.sphere.reg and lh.sphere.reg something that is created during the tutorial (ie is something wrong with my freesurfer installation that it cannot create these files), or are they simply missing from the tutorial subjects folder? I downloaded the tutorial package this week, and am using ubuntu 16.04 and freesurfer version 6. Any help would be greatly appreciated. Thank you.??

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Support with CVS/BBR Issue
by Austin Patrick 18 Feb '20

18 Feb '20

External Email - Use Caution Dear FreeSurfer Community, I have used the CVS and BBR registration methods to spatially align T1 and diffusion images to an ideal subject’s T1. I have noticed some discrepancies when viewing the aligned images in FSLview. If I toggle between subjects in FSLview the alignment looks quite good; however, when all subjects’ diffusion images are merged into a single 4D volume, the alignment is quite poor and variable. The same is true for subjects’ T1s. Is this a known issue and, if so, is it a problem with FSLview or my implementation of FreeSurfer? Thanks, -Austin -- Austin M. Bazydlo, MS PhD Candidate Dept. of Medical Physics University of Wisconsin-Madison

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hippocampal subfield segmentation - values for whole subfields
by Teresa Esteban 18 Feb '20

18 Feb '20

External Email - Use Caution Hello FreeSurfer Developers, I am trying to use the Hippocampal subfields tool (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAm…) to extract the stats of each subfield. On version v21 I obtain the stats for the subdivisions head, body and tail of different structures (i.e. CA1-body, CA1-head), but not of the undivided subfield (i.e. CA1). Would this undivided subfield be just the sum of the divisions? This is, would adding CA1-body and CA1-head give me the volume of CA1, or is there other way of obtaining it? I have searched the wiki and the list and I have not been able to find an answer. I would appreciate any insight! Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Thanks in advance, Teresa Teresa Esteban Predoctoral Researcher BCBL www.bcbl.eu t.esteban(a)bcbl.eu Tel: +34 943 309 300 Ext #215 Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer

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Difference bewteen beta and ces in FS-FAST
by Star Xi 18 Feb '20

18 Feb '20

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Re: [Freesurfer] Volume to 5th order icosahedron tesselation Surface (with PET images)
by Marina Fernández 18 Feb '20

18 Feb '20

External Email - Use Caution Hi Doug, We thought it would be better to use 5th order icosahedron tesselation for PET because the resolution of the volume is lower: If, for thickness analysis, we carry the structural volumes with a resolution of 1x1x1 to ico7 on the surface, with PET-volumes or connectivity maps (resolution of 2x2x2 or 3x3x3) we thought it would be more appropriate to use ico5 on the surface because in the surface transformation the interpolation of the data is lower. In addition the number of statistical comparisons is greatly reduced. Regards, Marina. Marina. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Hi experts, This is a question related to PetSurfer steps. I would like to know if it is correct to sample the mgx volume onto the surface of the average subject of my dataset (created with 5th order icosahedron tesselation) instead of the fsaverage (created with 7th order icosahedron tesselation) or if there is any problem in the next steps following this procedure. We would like to do that because the volume PET resolution is more proportional to this number of vertex (10242). Do you think it is correct? Best wishes, Marina. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> You could do it, but I would just use fsaverage. I don't understand what the relationship would be between the number of vertices on the surface and the number of voxels in the PET volume or the rational for using the 5th order ico

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Skull stripping quality assessment
by Adam Rytina 17 Feb '20

17 Feb '20

External Email - Use Caution Hello all, I want to assess the skull stripping quality performed in Freesurfer (autorecon1) and in FSL. Does any program enable to evaluate the skull stripping quality? If so, which metric is used for an evaluation?

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GLM DOSS question
by Ferraro, Pilar 17 Feb '20

17 Feb '20

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? 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? 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?). 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? 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? 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 Il giorno 16 feb 2020, alle ore 6:00 PM, freesurfer-request(a)nmr.mgh.harvard.edu<mailto:freesurfer-request@nmr.mgh.harvard.edu> ha scritto: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@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: Apply transformation (Adam Rytina) 2. A couple of questions (Zvi Baratz) ---------------------------------------------------------------------- Message: 1 Date: Sat, 15 Feb 2020 18:52:43 +0000 From: Adam Rytina <adam.rytina(a)outlook.cz> Subject: Re: [Freesurfer] Apply transformation To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <AM0PR0602MB33773F725E71511D519EA0409A140(a)AM0PR0602MB3377.eurprd06.prod.outlook.com> Content-Type: text/plain; charset="iso-8859-2" 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 <freesurfer-bounces(a)nmr.mgh.harvard.edu> za u?ivatele Douglas Greve <dgreve(a)mgh.harvard.edu> Odesl?no: sobota 15. ?nora 2020 17:15 Komu: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)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> 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/20200215/5… ------------------------------ Message: 2 Date: Sun, 16 Feb 2020 14:07:05 +0200 From: Zvi Baratz <z.baratz(a)gmail.com> Subject: [Freesurfer] A couple of questions To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CANJsFRZEX1H9D_9mTgP5mYh2Lfdr-GJQv69cvQh4=TS9p3e4Eg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" External Email - Use Caution Hi all, Thank you for all your amazing work! I started using FreeSurfer recently and there are a couple of questions I was hoping someone here might be able to help me with: 1. Does anyone know of any way to silence recon-all's output or redirect it to stdout when called programmatically through nipype? I tried a couple of different approaches (using python's os.devull and creating a fake file-handle that does nothing on write() calls), but I can't seem to be able to get rid of it. Also, and I apologize if it exists and I simply missed it, I think it would be great to simply add a --quiet flag or something of the sort, considering the output is anyhow saved to a log file. 2. Is there any more documentation on recon-all's output other that the ReconAllOutputFiles <https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles> page? I've noticed a lot of info is missing there. I would be more than happy to contribute to it myself but I'm not sure what resources I can use to gather more information, and also I'm having trouble finding the corresponding documentation files on GitHub. Thanks again and all the best! Zvi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20200216/4… ------------------------------ _______________________________________________ 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 22 *******************************************

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Postdoctoral Fellowship
by Didenur Sahin 16 Feb '20

16 Feb '20

External Email - Use Caution Dear All, Brain Development And Psychosis Lab, is pleased to announce the opening of a postdoctoral fellowship position in clinical neuroscience and cognitive neuroimaging. Please take a look at the attached advertisement. Best, Didenur Sahin -- Didenur Şahin Ph.D. Candidate Neuroscience Graduate Program National Magnetic Resonance Research Center (UMRAM) Bilkent University Ankara, Turkey 06800

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Freesurfer February 2020