Freesurfer

freesurfer@nmr.mgh.harvard.edu

18 participants
30131 discussions

Re: [Freesurfer] Annotation File to ROI Volume Estimate
by Jacoby, John 24 Feb '22

24 Feb '22

Hi Doug, thanks for the pointer. That was exactly what I was looking for. When I copied the command from recon-all.log, it used a -b flag. I can't find documentation for this flag either in the --help or on the wiki. Could you elaborate on what it does? Thank you! Best, John

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Dividing surface overlays
by Tisdall, Dylan 24 Feb '22

24 Feb '22

External Email - Use Caution Hi all, I've generated two surface overlays, using mri_vol2surf with positive and negative projfrac to get a GM and WM samples (gm_lh.nii.gz and wm_lh.nii.gz). I'd now like to take the vertex-wise ratio of these two overlays, and make a new one (gmwmratio_lh.nii.gz). I've tried doing this as: fslmaths gm_lh.nii.gz -div wm_lh.nii.gz gmwmratio_lh.nii.gz but the result is: Image Exception: #22 :: Failed to read volume gm_lh.nii.gz Error : Error: Nonsensical ROI for gm_lh.nii.gz Is there another tool I can use to compute this ratio? Is there a better workflow than making two surfaces and dividing? Thanks, Dylan

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SAMSEG "lesion" (Illegal instruction) ~ running VM_67
by daedalus39＠aol.com 24 Feb '22

24 Feb '22

External Email - Use Caution Dear Experts, I am trying to test SAMSEG "lesion" on VM_67 and after I entered: run_samseg --input /home/developer/subjects_new/o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T30-acc_orig__S689126_I1001975.nii /home/developer/subjects_new/rT1_o_ADNI_002_S_4654__MRI-m072__LMCI-LMCI__20180522__T2-FLAIR__S689135_I1001984.nii --pallidum-separate --lesion --lesion-mask-pattern 0 1 --output /home/developer/subjects_new/Lesion-test/ ...I got the following error Illegal instruction (core dumped) Is there anything glaringly wrong in my instruction/input phrase? Is SAMSEG "lesion" implemented in the new VM? I was able to test the "basic" SAMSEG with a single T1 earlier this morning (it ran just fine) Thanks in advance for any help. -Randy

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Mass-univariate LME - contrast for one group
by Franziska Haase 24 Feb '22

24 Feb '22

External Email - Use Caution Dear experts, Sorry, for posting again - I was not able to answer on my first post, don't know why. If anyone has an idea about this, please let me know! Unfortunately, I did not make any progress. Best, Franziska External Email - Use Caution Dear FreeSurfer experts, I am trying to use the spatiotemporal mass-univariate LME approach for my data but am struggling with choosing the right contrast. I have one group with 14 subjects, two timepoints for each subject and age. My goal is to test whether the subjects experienced any kind of change in cortical thickness from pre- to post-measurement, controlling for age. I followed the tutorial up to the point where I figured out that only one random effect is needed as most vertices did not survive multiple comparisons correction. If I am correct the next step is to test, whether a quadratic or a linear model is needed. Therefore, I tested the contrast CM1.C = [0 1 0 0] on my design matrix X with subjects, time in years, (time in years)², age: 1.0000 0 0 20.0000 1.0000 1.4800 2.1904 20.0000 1.0000 0 0 19.0000 1.0000 1.4800 2.1904 19.0000 ... Multiple comparisons correction revealed an empty vector (as in the tutorial), so that the quadratic term of time was removed and a linear model with one random effect is tested with the new design matrix 1.0000 0 20.0000 1.0000 1.4800 20.0000 1.0000 0 19.0000 1.0000 1.4800 19.0000 ... Next, I applied the contrast CM2.C=[0 1 0] to test for change over time. My question is if this is actually the right way to achieve my goal or whether I am doing something completely wrong. And if it is correct, I would go on by correcting for multiple comparisons, right? How would I visualize the results & additionally get information about significant clusters? Unfortunately, it seems like I am not understanding the last part of the tutorial. Any help would be much appreciated! Best, Franziska _____________________________ Franziska K. Haase, M.A. Sportmedizinisches Institut Department Sport und Gesundheit Fakultät für Naturwissenschaften Universität Paderborn Warburger Str. 100 33098 Paderborn Golfakademie 20b _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://secure-web.cisco.com/1ZxGOXwI-5I_nFKnzGJh-8sbjYxGtRJOXvHqwmkT48MJ8t…

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Error sending tcl command
by Yuhui LIANG 梁玉慧 24 Feb '22

24 Feb '22

External Email - Use Caution To whom it may concern, How are you recently? I am trying to follow the the ENIGMA Cortical QC protocol to check my external surface result after order "recon-all". The detail of scripts is attached bolow (here<http://secure-web.cisco.com/1dkHKFt2pSHfUZ0kA6gifWjCITDX34GWZl6d7V5zMMqr8bm…>). I used "tksurfer" to get a series of 4 images (.tif) files for each subject. But I always met this type of error. surfer: Error sending tcl command LblLst_UpdateInfo 33 "frontalpole" 32 1 100 0 100: invalid command name "LblLst_UpdateInfo" surfer: Error sending tcl command LabelsChanged: invalid command name "LabelsChanged" When I tried to solve this problem, I noticed that the "freesurfer" was cannot support "tksurfer" any more. In stead, they suggested users to run another command "tksurferfv" , which will run freeview with most of the "tksurfer" command line options. But both of tksurferfv and freeview can not support "tcl" command. The error is written as below. Everytime I trid to run this script, I always found this error. Option 'tcl' not recognized. By the way, I wanna notify you that I am using freesurfer version 7.2.0 in CentOS 8. How can I overcome this problem? Any advice would be appreciated! Sincerely, Yuhui

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PhD Position in Neuroimaging and Deep Learning at Karolinska Institute, Stockholm, Sweden
by Joana Braga Pereira 23 Feb '22

23 Feb '22

External Email - Use Caution Dear all, We are looking for a PhD student to work in an interdisciplinary and internationally competitive environment at Karolinska Institute, one of the top medical universities in the world and the home for the Nobel Prize in Medicine. We combine imaging analyses, statistical tools, machine learning algorithms, biofluid assays and genetics to study brain aging and the earliest signs of Alzheimer’s and Parkinson’s diseases. This project will be carried out under the supervision of Associate Professor Joana B. Pereira and it will involve applying methods based on deep neural networks to identify the anatomical and functional brain connections that are most vulnerable to Alzheimer’s disease and assess whether they can predict cognitive decline. The student will also have the opportunity to learn and apply computational models to identify the mechanisms responsible for the damage of brain connections in AD. Finally, the methods developed in this project in the second version of our software (BRAPH; http://secure-web.cisco.com/1Q2rgK7b8V70npiFIHUI8zfRjlE6qZiFHoTMy0cbxynHT1P…) which will soon be released. The ideal candidate should have the following qualities: - Background in computational science, neuropsychology, physics, statistics, medicine or a related field. - Experience in statistical techniques, programming, or scripting in MATLAB, Python and/or R. - Experience or interest in structural MRI, DTI, fMRI or PET imaging analyses. - Clinical or research experience with aging and/or neurodegenerative disorders are a merit. - Previous scientific publications are also a merit. The PhD studies will be performed for 4 years. For further information about my group and how to apply please go to: https://secure-web.cisco.com/1ajXNJ3Ewvrf48vViFvbFKr5slri9XmrpQLG9K2_LASnQX… The application deadline is 15/03/2022. If you have any questions please contact me at jbragapereira(a)gmail.com or joana.pereira(a)ki.se. Best wishes, Joana

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Incorrect SI/AP swap from bbregister
by Tisdall, Dylan 23 Feb '22

23 Feb '22

External Email - Use Caution Thanks for the help with my previous question on formatting the bbregister command line. Now that I've got it running, I'm seeing that 1 of my two subjects ends up with a 90 degree rotation (swapping SI and AP axes) when I try to register my 7T T1 or T2 scan to the surfaces from my 3T T1 scan. I've so far tried to analyze similar datasets from two subjects, and I'm only having this SI/AP swap in one of them (the second subject works great once I apply an initial transform to get it close) What steps should I take to try to understand what's going wrong? I've loaded the moving image into freeview, applying the initial transform as part of the load, and the result seems to align pretty closely with the surfaces when I load those as well... so I'd expect bbregister should align these well. Thanks again, Dylan

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cortical measurments
by REEM ABU BAKR BAHATHIQ 23 Feb '22

23 Feb '22

External Email - Use Caution Hello Freesurfer experts How can I get a text file of the cortical measurements of a group of images after they have been processed with recon -all?? Best, Reem

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convert .mgz to .nii
by REEM ABU BAKR BAHATHIQ 23 Feb '22

23 Feb '22

External Email - Use Caution Hello FreeSurfer experts, I want to run a classification task using deep learning on data processed by Freesurfer recon-all and I have some queries. I will use brainmask .mgz First of all, based on my simple knowledge, I cannot feed my model with this output directly. .mgz files must be converted to a .nii file for use in analytics. I found that this is done by writing mri_convert any_volume.mgz any_volume.nii.gz But how can I convert the files of all participants (more than 1000) into .nii files instead of going one by one? Are there any examples or tutorials provided to demonstrate the use of Freesurfer output in machine learning applications? My greetings,

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Re: [Freesurfer] GLM analysis - volume and surface area
by Laura Willers de Souza 22 Feb '22

22 Feb '22

External Email - Use Caution Thanks so much for the explanation! There is something different in the analysis of volume and surface area in relation to the analysis of cortical thickness? Like some more command, or some other detail that must be changed (besides, of course, the flag that specifies the measure to be analyzed) - I'm already using permutation in the correction of multiple comparisons. Best, Laura Willers de Souza Master Student in Biochemistry Zimmer Lab - Federal University of Rio Grande do Sul - Porto Alegre/RS - Brazil

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