Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30081 discussions

Re: [Freesurfer] Maps completely painted in freeview
by Laura Willers de Souza 04 Feb '22

04 Feb '22

External Email - Use Caution Sorry, I wrote it wrong! It was intercept contrast. Thanks so much for the explanation! Best, Laura.

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Re: [Freesurfer] mri_normalize error MP2RAGE
by Dr. Cornelius Kronlage 04 Feb '22

04 Feb '22

External Email - Use Caution > Can you send the recon-all.log file? Here you go, two examples. Thank you! Best Cornelius

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mri_concat error
by Mateus Aranha 04 Feb '22

04 Feb '22

External Email - Use Caution Dear all, I'm constantly getting the following error and I have no idea where the problem is... [image: image.png] Thanks for your help, Mateus

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Maps completely painted in freeview
by Laura Willers de Souza 04 Feb '22

04 Feb '22

External Email - Use Caution Hello FreeSurfer Developers, I am performing an analysis of the relationship between cortical thickness and cortisol, following exactly what is on the wiki https://secure-web.cisco.com/1FfPt4RYxp7QhaPPGponDxJJ_3LvYIPwa_msm03IO6Q5XZ… However, the uncorrected significance map for the interaction contrast is turning completely yellow, for both hemispheres. After correcting for multiple comparisons, the result is a whole-brain cluster, for both hemispheres too. The pcc.mgh map is also fully painted. But the maps for the slope contrast are correct. I am sending the fsgd file, the matrix files, the commands that I run and what appears on the command screen after running the commands to open the significance and pcc.mgh maps in freeview. (I'm not sending example images because my email has already been denied for being too big). Was this supposed to happen? Thanks in advance! 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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Unsure About Longitudinal & GLM Tutorials
by Edwards, Vincent 04 Feb '22

04 Feb '22

External Email - Use Caution Good morning Freesurfer Team! I would like to use GLM on my longitudinal study to measure change between two time points. I followed the longitudinal tutorial, and to my understanding, I would move on to the general glm tutorial next. The longitudinal tutorial says that "you can compare groups similar to a cross sectional analysis", but when we run stats on our significant clusters our results look "odd". I may have misunderstood the tutorial, but I plugged the longitudinal timepoints into my fsgd file like this: Input Subject1_TP1 subject 57 0.93 Input Subject1_TP2 subject 57 0.93 Input Subject2_TP1 subject 64 1.22 Input Subject2_TP2 subject 57 1.22 I'm not sure if what we ran is actually finding change between timepoints in our subjects. We happened across a glm paired-analysis tutorial. Should we re-run our data through that instead? The longitudinal tutorial only referenced the regular glm tutorial, so I want to make sure that we are following the correct steps - perhaps there is something I did wrong with my fsgd file? The paired-analysis tutorial seems like it may be appropriate, but I was hoping you could clear up our confusion before we move forward. Thank you, Vince

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lGI value aberrantly high, again
by Bernardoni, Fabio 04 Feb '22

04 Feb '22

External Email - Use Caution Dear all as some other posted before me, sometimes the computation of lGI fails with the message (see for example: https://secure-web.cisco.com/1LP2MjWSbRkQqjVjAMGGAySVoeFkdNhk1cYwhbxxVDmXiH…, https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9…, https://secure-web.cisco.com/1SX9AQfa4jGFVZg4d2lSYl8OLuP3FfkC_3AnJY2mfKP8J9…) 'lGI for vertex number 35901 of the outer mesh is 2.5958 ... remeasuring lGI value for vertex iV = 36001. It may take a few minutes. WARNING -- Problem for vertex iV = 36001, lGI value is aberrantly high (lGI=53.1127)... ...lGI computation will be stopped. This may be caused by topological defects, check mris_euler_number on the pial surface.' as many reported before me, computation of euler number gives 2, i.e. nothing wrong. another suggestion by marie schaer is to rerun recon-all -hemi ?h -autorecon2 -autorecon3 , with or without the -randomness option. The point is that the -randomness option seems to have no effect, the error occurs again in exactly the same place, with the exact same value (lGI=53.1127). I am using freesurfer 7.1. Has there been any development to solve this? Thank you in advance Fabio Bernardoni Dr. Fabio Bernardoni wiss. Mitarbeiter Division of Psychological & Social Medicine and Developmental Neurosciences http://secure-web.cisco.com/1xvuU9YpZrNAT8MBR8aeslCWdv2cNu-xhctWukMA-pgRDlf…; http://secure-web.cisco.com/18N9590xMz7PXy9R7etuq98MdgjKagN7Y04h0saKn6vRWYJ… +49 (0351) 458-5245 Universitätsklinikum Carl Gustav Carus an der Technischen Universität Dresden Anstalt des öffentlichen Rechts des Freistaates Sachsen Fetscherstraße 74, 01307 Dresden http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswP… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Katrin Erk Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113 http://secure-web.cisco.com/108KZKatqumySxQAcQhTRI4pLm-1UWBgP9aUo19kQxHoswP… Vorstand: Prof. Dr. med. D. M. Albrecht (Sprecher), Wilfried E. B. Winzer Vorsitzender des Aufsichtsrates: Prof. Dr. G. Brunner USt.-IDNr.: DE 140 135 217, St.-Nr.: 203 145 03113

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impact of defacing on eICV calculations
by Ritobrato Datta 04 Feb '22

04 Feb '22

External Email - Use Caution Hi All, I have inherited some T1 data that are defaced. If I run the defaced images through freesurfer, will that impact the eICV calculations ? Please let me know. Many thanks Ri

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Display PCC in cluster
by Andrei Bieger 04 Feb '22

04 Feb '22

External Email - Use Caution Hi, Douglas, I performed a group analysis and, after permutation, one cluster survived. How can I display this cluster over an inflated surface, but with colors representing the partial correlation coefficient? In other words, I would like to see the pcc.mgh file in an inflated surface, but only for those vertices belonging to the cluster. -- Andrei Bieger

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Co-Registration after recon-all
by m-maiworm＠web.de 04 Feb '22

04 Feb '22

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mri_normalize error MP2RAGE
by Dr. Cornelius Kronlage 04 Feb '22

04 Feb '22

External Email - Use Caution Dear freesurfer experts, when running recon-all (FS version 7.2.0) on skullstripped 3T MP2RAGE sequences, about 10-20% of scans from one scanner fail because of this: mri_normalize -g 1 -seed 1234 -mprage nu.mgz T1.mgz [...] Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 error: No such file or directory error: MRInormFindControlPoints: could not find enough control points error: No such file or directory error: MRInormFindControlPoints failed Command exited with non-zero status 253 nu.mgz as the input to mri_normalize looks good to me. I am of course happy to provide full logs and some example data - please let me know. The exact same problem (also MP2RAGE data) has been described twice before, but I couldn't find a solution: https://secure-web.cisco.com/1r3_UfItk0odyQTEjL22mLAxycj89_vXfN--AkpFwUzred… https://secure-web.cisco.com/1_dIFX4W-YMl78kLd-J9E7AGEkpzUy7zCtCTsFt-L6nLdA… Thanks you in advance and best wishes Cornelius

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