Freesurfer

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30088 discussions

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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A couple of questions
by Zvi Baratz 16 Feb '20

16 Feb '20

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

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About statistical analysis of volumetric results
by Halil Aziz VELİOĞLU 15 Feb '20

15 Feb '20

External Email - Use Caution Hi Mr/Mrs We treated a group of patients. We performed volumetric analysis in freesurfer before and after treatment. Is it correct to take volumetric values directly into a paired test? Or should we perform statistical analysis after dividing all values before and after treatment by "Estimated Total Intra Cranial Vol"? Is normalization by doing this way? Best regards Halil Aziz -- Öğr. Gör. Dr. Halil Aziz Velioğlu Kognitif Sinirbilim Anabilim Dalı

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ROI Analysis in a given label with Functional Constraint in FSFAST
by Star Xi 15 Feb '20

15 Feb '20

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Re: [Freesurfer] Cluster-wise correction for multiple comparisons
by Kim, Gwang-Won 14 Feb '20

14 Feb '20

Dear Douglas N. Greve, Thank you very much for your email. I ran mri_glmfit without --wis. Then I tried to ran mri_glmfit-sim as following: mri_glmfit-sim -glmdir g2v3.wls -2spaces -perm 1000 1.3 abs. But there is an error message “ERROR: design matrix is not orthogonal, cannot be use with permutation. If this something you really want to do, run with -perm-force”. How can I do if I want to solve this problems? Thanks, Gwang-Won ----------------------------------------------------------------------------------------------- Message: 6 Date: Fri, 14 Feb 2020 09:42:28 -0500 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Cluster-wise correction for multiple comparisons To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <fd8cd06d-6bcf-a108-4fbe-52080d93cf83(a)mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" You don't need to specify a mask when you run mri-glmfigt-sim. When you ran mri_glmfit, you already specified the mask and that gets stored in the glmdir and then read by mri_glmfit-sim. Your mri_glmfit-sim command line look right (but you don't need the --bg 1 unless you really want to background the process, but using only one process will not speed it up). the other thing I want to point out is that (pseudo) weighted-least squares will not be taken into account by the permutation. I would rerun mri_glmfit without --wls and then run mri_glmfit-sim On 2/7/2020 3:01 PM, Kim, Gwang-Won wrote: > > Hi there, > > First, I ran "mri_glmfit" using mask including 4 ROIs(file name: > 4_ROI.label) as follows: mri_glmfit --glmdir g2v3.wls --y ces.nii.gz > --wis cesvar.nii.gz --fsgd 2group.fsgd --C group.diff.mtx --lable > 4_ROI.label? --surface fsaverage lh - --fwhm 5 ?eres-save. > > Second, I'm going to process "mri_glmfit-sim" to perform a > cluster-wise correction for multiple comparisons. > > Please let me know how to process "mri_glmfit-sim" using masks (file > name: 4_ROI.label) . > > Is it right? ?mri_glmfit-sim --glmdir g2v3.wls --perm 1000 3 abs > --2spaces --bg 1? > > Thank you, > > Gwang-Won >

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Pial surface not including parts of cortex
by Monica Bondy 14 Feb '20

14 Feb '20

External Email - Use Caution Dear Freesurfer experts, I was wondering if I could get some help with a problem that I keep experiencing. For some of the patients, their gray matter is not properly included in the pial surface. I have tried tkmregister and using control points but neither have been successful. I have read on a separate thread that editing the wm.mgz may be helpful but could I have some guidance on this please? Also, I know it can be difficult to tell the problem based on the description so please let me know if I can send something over to help. I'm still very much learning how to work freesurfer so I really appreciate your help. (Note: I am using version 5.3) Thank you, Monica

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make average subject/ highres fMRI data
by Nasiriavanaki, Zahra 14 Feb '20

14 Feb '20

Dear Freesurfer experts Hi I got an error when I was trying to make an average subject. I attached the log file. I appreciate if you could please let me know what the problem is. make_average_subject --out avgsubject --subjects subj1 subj2 subj 3 labeling Slice relabeling unlikely voxels in interior of white matter mri/norm.mgz: could not load norm volume from Linux bee.nmr.mgh.harvard.edu 3.10.0-1062.4.3.el7.x86_64 #1 SMP Wed Nov 13 23:58:53 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux recon-all -s avgsubject exited with ERRORS at Mon Feb 10 10:43:37 EST 2020 For more details, see the log file /autofs/space/oprah_001/users/zn025/looming_7T/SUBJECTS_DIR/avgsubject/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Request for access to the freesurfer mailing list
by Varun Chandran 14 Feb '20

14 Feb '20

External Email - Use Caution Dear Freesurfer committee, I would like to use the freesurfer mailing list to post my doubts about the cortical thickness analysis pipeline. Therefore, could you please provide me the access to post my doubts on the same? thanks, kind regards, Varun Arunachalam Chandran PhD in Neurosciences, School of Psychology and Language Sciences, University of Reading, Berkshire, UK

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