Freesurfer June 2022

freesurfer@nmr.mgh.harvard.edu

84 participants
123 discussions

Surface normalization
by Rafael Navarro 01 Jun '22

01 Jun '22

External Email - Use Caution Hello FreeSurfer Developers, I am building a brain age model from the stats extracted with FreeSurfer. I tested my model normalizing volumes by eTIV, which I think is the recommended, and surfaces by WM total surface. For surfaces, I haven't found any recommendations. I am getting better results by using the features without normalization. From what I have read, volume normalization clearly should be performed, but I am in doubt about the surface normalization. Although, the surface is different depending on head size and along with lifespan, I am not sure if all cortex surfaces evolve the same way, and therefore that normalization might be adding noise to my results. Then, is it correct to normalize my surface features by the total WM surface? Does anybody know any reference that talks about the topic or have done similar work? Thank you for your support ----------------------------------- || Rafael Navarro González || Ph.D. Student || ETSI Telecomunicación || Universidad de Valladolid || Campus Miguel Delibes || 47011 Valladolid, Spain || e-mail: rafael.navarro(a)uva.es || Phone: +34 672 394 294 ||_________________________________ -----------------------------------

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Now accepting applications for MSc Applied Neuroscience at Royal Holloway, University of London
by Joe.Bathelt 01 Jun '22

01 Jun '22

External Email - Use Caution **APPLY NOW FOR MSC APPLIED NEUROSCIENCE IN ONE OF HIGHEST RATED PSYCHOLOGY DEPTS IN THE UK** MSC APPLIED NEUROSCIENCE - Department of Psychology, Royal Holloway, University of London * You can gain a unique insight into the ways that Neuroscience techniques can be used in real world settings – with hands-on experience across a range of applied neuroscience techniques taught by leading experts * Exciting career opportunities such as user experience, digital design and marketing, immersive technology, data science, research or a PhD! * Applications encouraged from undergraduates in related Psychology/Cognitive Science/Biology/Computer Science/Physics/Mathematics * https://secure-web.cisco.com/1Ks48yyW-4KxFhlRXaR4GBM2FwuZSePvnHvWq80M5uZutu…<https://secure-web.cisco.com/1Pb57hF7a9UBX7ENNpSFL9SB9z3tI4NaNEK_CJjY_dgbjH…> This email, its contents and any attachments are intended solely for the addressee and may contain confidential information. In certain circumstances, it may also be subject to legal privilege. Any unauthorised use, disclosure, or copying is not permitted. If you have received this email in error, please notify us and immediately and permanently delete it. Any views or opinions expressed in personal emails are solely those of the author and do not necessarily represent those of Royal Holloway, University of London. It is your responsibility to ensure that this email and any attachments are virus free.

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Custom LUT
by Benjamin Deck 31 May '22

31 May '22

External Email - Use Caution Hi freesurfer experts, I am attempting to create a custom LUT from a parcellation I created. I have projected the labels into the subject's volume space and then concatenated all of these volumtes together using: mri_concat --sum --f vols.txt --o sub_vols.mgz When I visualize these on the subject's t1w the number of ROIs looks approximately correct (n~105). However, my custom LUT seems to be incorrect. Not sure how that is. I used the FreesurferLUT as my template and added new colors and changed names of each row to match my file names (excluding the .mgz). Here is my custom LUT 0 Unknown 0 0 0 0 1 Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 5 5 5 5 2 Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 25 5 25 0 3 Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 25 100 40 0 4 Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 70 130 180 0 5 Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 100 100 0 0 6 Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 196 58 250 0 7 Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol 100 25 0 0 8 Net_12_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol 120 70 50 0 9 Net_13_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol 220 20 10 0 10 Net_13_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol 220 20 100 0 11 Net_13_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol 180 40 120 0 12 Net_13_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol 122 186 220 0 13 Net_13_ROIs_3_lh_native_sm6_sm6_dil2_lh_vol 140 20 140 0 14 Net_13_ROIs_3_rh_native_sm6_sm6_dil2_rh_vol 12 48 255 0 15 Net_13_ROIs_4_lh_native_sm6_sm6_dil2_lh_vol 20 30 140 0 ------and it goes on for 105 indices. here is my list of volumes Net_10_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_19_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_10_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_2_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_11_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_2_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_11_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_2_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_12_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_2_ROIs_2_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_12_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz Net_3_ROIs_1_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_12_ROIs_2_lh_native_sm6_sm6_dil2_lh_vol.mgz Net_3_ROIs_1_rh_native_sm6_sm6_dil2_rh_vol.mgz -------and so on. Below I show that you can load each volume onto the brain and pick individual colors. [image: image.png] However, when I load the concatenated brain and load my custom image. All of ROIs get listed one of two ROIs. [image: image.png] Any guidance on this odd behavior would be much appreciated. Thanks, Ben OS: Windows--WSL2 Ubuntu 18 FS version: freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b -- *Benjamin L. Deck* *Doctoral Student* *Applied Cognitive and Brain Sciences* *Department of Psychological and Brain Sciences* *Drexel University* <https://secure-web.cisco.com/19Zn9eBKlEcFDurLHH9K8qOmPXm76HWXsKoN-XxABNV__4…> Virus-free. http://secure-web.cisco.com/17nfhwzVH4FamivxxfM5csvgLADzPjVc-AdC_7JKlsJRQMF… <https://secure-web.cisco.com/1E0laxvnp9bhVNgWasuocl4hqSjGHLHVu2yD3TqEvK6dfc…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Freesurfer June 2022