Freesurfer June 2018

freesurfer@nmr.mgh.harvard.edu

105 participants
154 discussions

Can freesurfer work well to T1 images without TR/TE/TI and flip angle information？
by He Chen 18 Jun '18

18 Jun '18

External Email - Use Caution Hi freesurfer experts, The recon-all command was conducted to my data by: recon-all -all -s sub1 -i anat.nii . But freesurfer seems to not be able to read the TR/TE/TI and flip angle information in the .nii file. Or there is no information about TR/TE/TI or flip angle stored in the .nii file. Although the terminal told me recon-all finished without errors, I think there still may be some implicit and fatal errors. I want to know whether all the processing steps in 'recon-all -all' command can work appropriately without TR/TE/TI and flip angle information? See the recon-all.log file: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ... reading from /media/emily/DATA_Storage/test_freeview/sub1/mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 ... recon-all -s sub1 finished without error at Fri Jun 15 04:36:11 CST 2018 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Thank you! He

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Re: [Freesurfer] Questions regarding Permutation and Monte Carlo simulation
by Douglas N. Greve 18 Jun '18

18 Jun '18

Hi Lea, I'm cc'ing the list so that others can benefit. On 06/13/2018 12:28 PM, Backhausen, Lea wrote: > > > Hey Doug, > > Thanks for your helpful suggestions on Monte Carlo simulation and > permutation you gave in the Mailing List! > > I have some follow-up questions, also regarding your recently > published paper about false positive rates > (https://www.sciencedirect.com/science/article/pii/S1053811917310960) > > 1) Concerning Monte Carlo simulation where you said even 1000 > iterations would be okay: What will the difference be between 1000 and > 10,000 iterations? I read in the tutorial that >5000 are recommended? > This has to do with the precision of the cluster p-value Since you are doing a simulation, the p-value is subject to sampling error. If you look in the output file, you will see that I give 95% confidence intervals for the p-value, so as long as the high range is less than .05, then it should be ok. I think 1000 is probably fine. > > 2) In your paper you write that permutation requires that data is > exchangeable across subjects and that age effects may be a problem. In > our study we want to compare adolescent patients with ADHD and conduct > disorder with typically developing adolescents. In this context, data > would not be exchangeable across subjects, right? Could we still use > permutation? > Exchangeability is a very complicated subject and not very intuitive. It is too complicated to get into here. I suggest reading up on it a little. It does not mean that you can swap groups without there being any effect. > > 3) When using the CFT thresholds with Monte Carlo simulation you > recommend in your paper, do you still only report clusters with > CWP<.05 or is the CWP less important when using stricter thresholds? > Generally, CWP must be less than 0.05 for publication. Sometimes people will show results with more liberal p-values (eg, 0.1) to show "trends". It all depends on what you can get past your reviewers:). doug > > Thank you so much for your input! > > Best > > Lea Backhausen > > ------------------------------ > > Lea Backhausen > > Research Assistant > > Department of Child and Adolescent Psychiatry, Faculty of Medicine of > the TU Dresden, Germany > http://www.uniklinikum-dresden.de <http://www.uniklinikum-dresden.de/> >

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mri_glmfit ERROR no voxels found
by Marine Boudot de la Motte 18 Jun '18

18 Jun '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to do a Surface-based analysis on Freesurfer while projecting MTR MRI sequences. I have followed all the steps explained in the group analysis tutorials, and the mri_preproc seems to have ran correctly but once the mri_glmfit is launched i get the following error : Computing normalized matrix Normalized matrix condition is 38.1502 Matrix condition is 1.78431e+12 Found 149926 points in label. Pruning voxels by thr: 1.175494e-38 Found 0 voxels in mask ERROR: no voxels found in the mask make sure at least one voxel has a non-zero value for each input I've searched the list but didn't find an answer. Does anyone have any clue on how to solve this problem ? Thank you very much for your help, Marine

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Re: [Freesurfer] Longitudinal analysis of multiple scanner acquisitions
by zalewk 18 Jun '18

18 Jun '18

External Email - Use Caution Hello Freesurfer Team, Sorry to bother you guys again, any word on what you think is the best approach going forward here? Best, Kody Zalewski ________________________________ From: zalewk Sent: Thursday, June 7, 2018 10:39 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Longitudinal analysis of multiple scanner acquisitions Good afternoon Freesurfer team, I want to run the longitudinal pipeline on multiple groups of subjects, the problem is we are at the mercy of the scanners available to us at the various time-points. We have two different Siemens 1.5 scanners (same type of scanner, there was an effort made to match them) at time point 1 and 2 with a Phillips 3T at time point 3. Is it worth the time to attempt a longitudinal analysis on this cohort? Best, Kody Zalewski

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Running qcache on old FS data
by Jamie Hanson 18 Jun '18

18 Jun '18

External Email - Use Caution Hello all, I was trying to run qcache on some previously processed Freesurfer data from a colleague, but ran into some issues with missing files and wondered how best to proceed. Details: -The data was processed with (Freesurfer) v4.5.0 and I would ideally like to not reprocess it with a newer version (to keep in concordance with past published work, and also it's a large number of subjects, n=800+). -The qcache flag was not used with the data previously (to my knowledge), so I was attempting to run this command: recon-all -s $subj -qcache -When I try that command, I get an error regarding a missing lh.white.K file. I've uploaded the log file here: https://www.dropbox.com/s/94mnsy7wrps5ce2/recon-all.log?dl=0 I wondered if it was possible to complete qcache with the data as is? I searched on the list previously and saw one or two other folks had run into this issues; I, however, didn't see a final solution to things. Any thoughts or suggestions are greatly appreciated! Thanks much! Best, Jamie. -- Jamie Hanson Assistant Professor, Psychology Research Scientist, Learning Research and Development Center University of Pittsburgh Personal website: jamiehanson.org

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Recon-all exited with errors
by Ryan Flores 18 Jun '18

18 Jun '18

External Email - Use Caution Dear FS developers, I tried running recon-all using the -parallel flag over the weekend, but to my surprise they all exited with errors. I’m hoping the problem is something subtle, but I’m having trouble understanding the error log (please see attached). Can someone point out the issue? Thank you for your help. Best, Ryan -- Ryan Flores Clinical Research Coordinator

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Can freesurfer do SC (superior colliculus) segmentation?
by He Chen 17 Jun '18

17 Jun '18

External Email - Use Caution Hi all, I need ROIs of SC(Superior Colliculus). Can freesurfer distinguish it from other brainstem structures in segmentation? I also need to see responses of distinct layers of SC. Can freesurfer do layers segmentation according to the distance between each voxel and SC surface layer? That is, I need ROIs of different depth in the SC. The depth should be calculated by the distance from the voxel to SC surface. How to modify the 'recon-all -all' code if I just need the segmentation function mentioned above? Please forgive the ignorance of a freesurfer beginner. Thank you in advance! Chen He

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Contrast interpretation - between-groups mean
by Pedro Rosa 16 Jun '18

16 Jun '18

External Email - Use Caution Dear FreeSurfers, I got results from a cortical area analysis that intrigued me: Upon the inspection of clusters that survived Monte-Carlo simulation, I found a cluster with larger area among a first group in contrast to a second group. However, when I calculated the cortical areas means from that cluster (as available in the glmdir), the second group had values slightly larger than the first group (i.e., showing a difference in the opposite direction). How would you explain such findings? Must I have committed a mistake in the analysis or its interpretation? Best, Pedro Rosa - University of São Paulo - Brazil.

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mri_gtmpvc
by Alshikho, Mohamad J. 15 Jun '18

15 Jun '18

Dear Dr Greeve, Kindly, I'd like t to inquire about the command "mri_gtmpvc" in PET surfer. Can I use this command to apply partial volume correction on non-PET data (e.g. DTI or ASL)? Thanks! Mohamad

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TotalGrayVol and SubCortGrayVol for multiple subjects
by Fernanda Hansen P. de Moraes 15 Jun '18

15 Jun '18

External Email - Use Caution Good morning all, I want to get the TotalGrayVol and SubCortGrayVol for multiple subjects. Is there any flag that I can use with asegstats2table? Or how should I use mri_segstas to creata a new aseg.stats file for my subjects? If that's the case, how should I define the output file from mri_segstats so asegstats2table can read it? Thank you very much in advance, Fernanda Hansen P. de Moraes -- Fernanda Hansen P. de Moraes Física Médica | Instituto D'Or de Pesquisa e Ensino | Rede D'Or São Luiz

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Freesurfer June 2018