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POSTDOC and PhD POSITION- photoacoustic imaging , machine learning and OCT image analysis
by Nasiriavanaki, Zahra 24 Aug '20

24 Aug '20

Hi all Please see below for available postdoc and PhD positions at the Biomedical Engineering Department, University of Illinois at Chicago. Best, Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129 We have openings for two postdocs, one with expertise in the area of photoacoustic imaging instrumentation, and the other one in the area of machine learning and OCT image analysis. We also have one Ph.D. position available in the area of photoacoustic imaging. Please share this with your qualified colleagues/friends. See more details at: https://engineering.academickeys.com/seeker_job_display.php?dothis=display&… [http://engineering.academickeys.com/seeker_job_attachments.php?dothis=displ…]<https://engineering.academickeys.com/seeker_job_display.php?dothis=display&…> Two postdoctoral positions and a PhD position at the Biomedical Engineering Department , Biomedical Engineering Department , The University of Illinois at Chicago (UIC)<https://engineering.academickeys.com/seeker_job_display.php?dothis=display&…> Two postdoctoral positions and one PhD position are available in OPIRA lab in the Biomedical Engineering Department, the University of Illinois at Chicago (UIC). 1. The first postdoctoral fellow will contribute to the design, development, and optimizati... engineering.academickeys.com<http://engineering.academickeys.com/>

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Re: [Freesurfer] extracting beta coefficients and p-values
by Douglas N. Greve 24 Aug '20

24 Aug '20

answers below. also, please remember to post to the list On 8/21/2020 6:52 PM, Rizvi, Batool wrote: > > External Email - Use Caution > > Thank you Dr. Greve! This is very helpful! Just to confirm, similar to > taking the effect of age, if I wanted to get the beta of Parietal WMH > (my main continuous IV), I would just average betas 5-8? > > I forgot to add this in my previous email, but I’m also trying to > extract p-values of all the variables involved, and wasn’t sure how > to. I tried running a couple different commands. > > When I ran this below command, I got a file with 1 column of 8 numbers: > > mri_segstats --i contrasts.sig.mgh --annot fsaverage lh > lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot > --excludeid 0 --avgwf avgwfsig.dat > where did contrasts.sig.mgh come from? Was this created by QDEC? > > But when I tried the below command, I got a file with 1 number. > > mri_segstats --i lh-Avg-long.thickness-spc-Parietal_WMH-Cor/sig.mgh > --annot fsaverage lh > lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot > --excludeid 0 --avgwf avgwfsig2.dat > > From the 1^st way (using contrasts.sig.mgh): > > -0.27711 > > -2.51072 > > 0.42697 > > 0.62922 > > -0.85069 > > 0.52623 > > 1.00393 > > -0.42921 > > From the 2^nd way (using sig.mgh) > > -2.51072 > > I’m pasting my fsgd format once more: > > GroupDescriptorFile 1 > > Title ParietalWMH_age_gender_APOe_EC_left > > MeasurementName long.thickness-spc > > Class APOE_statusNO-genderF > > Class APOE_statusYES-genderF > > Class APOE_statusNO-genderM > > Class APOE_statusYES-genderM > > Variables Parietal_WMH age_years Avg_ECthickness > > Input W38284_base APOE_statusNO-genderF 0.732010 85.830000 3.125000 > > .. (only listing the 1^st Input line here) > > My contrast file (C.dat) looks like below: > > 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 > > And I’m trying to find p-values for these variables’ associations w/ > thickness: APOE status, gender, Parietal WMH, Age, Avg EC thickness. > Each contrast will have a sig file. But the command above will compute the average significance, which really does not mean anything > > Thanks so much again for all the help! > > Batool >

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problems with brainmask.mgz and wm.mgz files
by Dalton Bermudez 24 Aug '20

24 Aug '20

External Email - Use Caution For some reason when I ran the recon-all command it generated a brainmask.mgz file which excluded part of the right hemisphere and a wm.mgz which did a horrible job at segmenting gray matter from white matter. The recon-all command later exited with an error. How do I fix the problem? I have attached the recon-all.log file for your reference. Thank you, Dalton

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FreeSurfer6 hires patch for longitudinal output
by Nandita Vijayakumar 24 Aug '20

24 Aug '20

External Email - Use Caution Dear FreeSurfer team, I have processed my data through the longitudinal stream of FreeSurfer6 using the -hires flag. I would like to apply the patch to fix the global metrics, but seem to run into an error when supplying the longitudinal subject directory. I've tried running the following command: recon-all -long sub-001_wave1.long.sub-001 sub-001 -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels But get the following error: Unmatched ". The command seems to work fine on the cross-sectional directories. So I'm wondering if the patch can be applied to longitudinal directories? Thanks, Nandi

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Segmentation Labels for the Skull
by mudassar liaq 24 Aug '20

24 Aug '20

External Email - Use Caution Hi, (A but of a dumb question but) Is there any way we can also have skull also labeled () along with the brain parts in MRI output? [image: image.png] * Skull mentioned by white arrows Thanks and Regards,

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recon-all exited with error
by Dalton Bermudez 23 Aug '20

23 Aug '20

External Email - Use Caution ERROR: MultiRegistration::loadMovables: images have different voxel sizes. Currently not supported, maybe first make conform? Debug info: size(1) = 1, 1, 1 size(0) = 1, 0.976562, 0.976562 error: No such file or directory error: MultiRegistration::loadMovables: voxel size is different /home/dbermudez/Documents/subjects/00_0001/mri/orig/002.mgz. However, I have checked the dimensions of both the T1w and the T2w and they both have the same dimensions: 176×256×256. I do not know what is the problem? and how can I fix the issue?

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FastSurfer with FreeSurfer version 7.1.0?
by Billah, Tashrif 22 Aug '20

22 Aug '20

Hi Barbara and Martin, I didn't have any problem running FastSurfer with FreeSurfer 7.1.0 either. Best, Tashrif

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ROI-wide cortical thickness for each network !
by Martin Juneja 22 Aug '20

22 Aug '20

External Email - Use Caution Hi experts, I extracted network-wise cortical measures (i.e., 7 cortical thickness values for 7 networks for Yeo atlas). I was wondering if there is a way to get the cortical thickness of each ROI within each of these networks e.g., cortical thickness values of all the ROIs which constitute default-mode network of Yeo's 7 network parcellation, and then cortical thickness values of all the ROIs which constitute limbic network of Yeo's 7 network parcellation, and so on. I know Desikan atlas can be used to get morphometry measures of 34 ROIs per hemisphere. But the problem is that e.g., default-mode ROIs from Desikan atlas do not completely overlap with the DMN of 7-network parcellation from Yeo atlas. In other words, superior frontal cortex from default-mode network of Yeo 7 network parcellation is a big chunk compared to several small ROIs (some partial and some full) in Desikan atlas, so I do not see any way how to find ROIs which just match with that superior frontal cortex of default-mode of Yeo's 7 network. Any help would be much appreciated !

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How to run recon-all for different subjects and each subject with different sessions ?
by Camargo, Aldo 21 Aug '20

21 Aug '20

External Email - Use Caution Hi Freesurfer experts, I have a question: How to run recon-all for different subjects and each subject with different sessions ? Thanks a lot in advance and have a nice day, Aldo

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extracting beta coefficients and p-values
by Rizvi, Batool 21 Aug '20

21 Aug '20

External Email - Use Caution Dear FreeSurfer experts, After running the longitudinal pipeline with QDEC, I needed beta-values of the associations between my main continuous variable and the significant cortical cluster, as well as of all the nuisance factors/categorical variables. Since the summary file doesn't list beta values, I attempted running this command to find beta coefficients: mri_segstats --i beta.mgh --annot fsaverage lh lh-Avg-long.thickness-spc-Parietal_WMH-Cor/mc-z.abs.th20.sig.ocn.annot --excludeid 0 --avgwf avgwf.dat >From this, I got this output file listing beta values for 1 cluster (entorhinal cortex) that was related to my main continuous IV (parietal WMH). I'm struggling to understand how to still compute 1 beta-coefficient per variable from this list. I understand that this list, based on my fsgd file, can be split into 4 sets of numbers, but I'm not sure what do next. avgwf.dat: 0.93879 -8.80748 0.38452 3.13252 -0.09493 -0.13107 -0.09960 -0.31087 -0.02291 0.03127 -0.02417 -0.07858 0.13087 1.80749 0.32535 0.64947 Below is how my fsgd file was structured: GroupDescriptorFile 1 Title ParietalWMH_age_gender_APOe_EC_left MeasurementName long.thickness-spc Class APOE_statusNO-genderF Class APOE_statusYES-genderF Class APOE_statusNO-genderM Class APOE_statusYES-genderM Variables Parietal_WMH age_years Avg_ECthickness Input W38284_base APOE_statusNO-genderF 0.732010 85.830000 3.125000 .. (only listing the 1st Input line here) My contrast file (C.dat) looks like below: 0 0 0 0 1 1 1 1 0 0 0 0 0 0 0 0 So basically, I would like to get beta coefficients for the below variables: * Parietal WMH * Age * Gender * APOE status * Average EC thickness (baseline values) Thank you so much in advance for your help! Batool

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