Freesurfer

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30083 discussions

Main effect of sex for total surface area, but not for summed vertex-wise surface area
by Linn Christin Bonaventure Norbom 08 Oct '19

08 Oct '19

External Email - Use Caution Hello all Freesurfer experts! Through my analysis I found that, if I plot the "white surface total area" found in subjid/stats/?h.aparc.stats by sex, I as expected find that males have overall larger surface area as compared to females. When plotting the summed verticies of ?h.area for each person on the other hand (albeit after mapping the ?h.area to fsaverage), this main association with sex is not at all present. I am a bit puzzled by this and I am wondering if some sort of global scaling is performed when computing vertex-wise surface area? So that corresponding differences in vertex-wise area are relative sex differences? I understand that area at a single vertex does not hold biological relevance in the same way that for instance thickness does, but unfortunately I still don't quite understand the differing sex associations between aparcs total surface area and the summed vertex-wise surface area. Thanks so much in advance! Kind regards Linn

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Accessing the FS mail archive online
by Adam Martersteck 08 Oct '19

08 Oct '19

External Email - Use Caution Hi Freesurfer team, Just in case this hasn't been brought to your attention -- it looks like the online mail archive requires a martinos center login. Accessing links to past questions and answers via google or just https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ prompts for a login. I can replicate this on multiple computers, phones, on and off different VPNs. It's been happening for the last week or two. -Adam

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Read out N from mri_glmfit outputs?
by Caspar M. Schwiedrzik 08 Oct '19

08 Oct '19

External Email - Use Caution Hi! Is there a way to read out the N of a fixed effects analysis performed with mri_glmfit? If not, is it safe to assume that it is (number of volumes*number of runs)-excluded time points, summed across subjects? Thanks! Caspar

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Re: [Freesurfer] ERROR gtmseg
by Marina Fernández 08 Oct '19

08 Oct '19

External Email - Use Caution Dear Douglas, Sorry! This is the previous information: > Dear Douglas, > > Thank you for the replay. > > I think so, I can't find the code 229 in any subject. > > I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels have the normal > > segmentation and labels. Could it be a problem with the extracerebral voxels? > > Best regards, > Marina. > That is kind of weird. It says it has found a segmentation with number > 229, but we don't have that code in our system. Can you find the 229 voxels > in the aparc+aseg.mgz? > Dear experts, > > The following error occurs with one subject when I am running gtmseg > command: > > Computing colortable > ERROR: cannot find match for subcortical segid 229 > ERROR: mri_gtmseg -s qsm_04_year3 --usf 2 --o gtmseg.mgz --apas > apas+head.mgz --no-subseg-wm --no-keep-cc --no-keep-hypo > gtmseg existed with errors > ans=1 > > Do you know what happened with this subject? What can I do to solve it? > > Thank you very much in advance. > Marina.

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negative values of hippocampal subfields volumes
by Krzysztof Gbyl 08 Oct '19

08 Oct '19

External Email - Use Caution Hi all, I am currently running a longitudinal hippocampal subfields analysis using version 6.0. Based on the visual inspection of images, I see that Freesurfer is doing a great job. The problem is that I get negative values of the subfields volumes e.g. Hippocamap_tail -420.400366 subiculum -368.134590 The values seems to be reasonable, but why they are negative, i.e. why they have a '-' sign. Could the minus sign be a hyphen? Has anybody encounther this problem? I hope you can help BW, Chris

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FreeSurfer freezing during processing.
by Троицкий Антон Александ рович 07 Oct '19

07 Oct '19

External Email - Use Caution Hello FreeSurfer Developers, I have installed the FreeSurfer how described here https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport. I launch an Ubuntu terminal and stat a freesurfer application from an Ubuntu command line. [cid:4348455d-9967-4416-9824-c67b83e00ac4@fccho-moscow.ru] I can see in a task manager that different tasks are working and the processing is going. I can see the output in the ubuntu terminal and see the last steps of processing. I don’t know exactly when but after some period of time the processing is freezing and paused. It is really strange because I don’t see any task in the task manager associated with the processing of. It lasts a while and I decide to stop the processing by using ctrl+c. And it is so strange the processing continues after that. It happened twice for the same dataset. I have launched the processing of test data sample-001.nii.gz. It is going well. I have two different datasets that have been processed on the other station and the processing was completed without errors. It is an output in recon-all.cmd file #@# EM Registration Thu Oct 3 09:51:44 MSK 2019 mri_em_register -rusage /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/ #@# CA Normalize Thu Oct 3 11:42:10 MSK 2019 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /usr/local/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz #-------------------------------------- #@# CA Reg Thu Oct 3 11:43:49 MSK 2019 mri_ca_register -rusage /usr/local/freesurfer/subjects/2019-07-22_3DBrainView_T1_2019-10-03_09-18/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /usr/local/freesu$ Is it normal that the process mri_em_register was going so long? And it continued after I pressed the ctrl+c command. Is it normal this behavior of processing of the data? How do you think what is the cause of this kind of behavior of the processing? Does anybody try to do it? I have found this way for parallel processing. https://andysbrainbook.readthedocs.io/en/latest/FreeSurfer/FS_ShortCourse/F…. But it is not the same. Best regards, Anton Troitskii.

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Question about using tkregisterfv to check registration
by Vicky Yang 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Freesurfer experts, I used mri_coreg to register my pet data to T1 like below: mri_coreg --mov pet.nii.gz --ref T1.nii --reg pet_T1.reg.lta After coregistering, I checked the registration using tkregisterfv like below: tkregisterfv --mov pet.nii.gz --targ T1.nii --reg pet_T1.reg.lta However, the command didn't work with an error: if: Expression Syntax. Any suggestions would be appreciated. Thank you in advance for your help. Sincerely, Vicky

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Re: [Freesurfer] ERROR gtmseg
by Marina Fernández 07 Oct '19

07 Oct '19

External Email - Use Caution Dear Douglas, Thank you for the replay. I think so, I can't find the code 229 in any subject. I can't see anything strange in the aparc+aseg.mgz. The cerebral voxels have the normal segmentation and labels. Could it be a problem with the extracerebral voxels? Best regards, Marina.

2 1

Confidence interval for Cohen's d from gamma/rstd
by Caspar M. Schwiedrzik 07 Oct '19

07 Oct '19

External Email - Use Caution Hi! I have an OSGM from a fixed effects group analysis with mri_glmfit. I would like to calculate the effect size and the 95% confidence intervals. I see from various threads on the mailing list that Cohen's d can easily be obtained from the outputs of mri_glmfit by dividing gamma by rstd. I am wondering now how to compute the 95% CIs for Cohen's d from the outputs of mri_glmfit? Thank you very much! Caspar

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Comparing effects between voxels in a FFX GLM
by Caspar M. Schwiedrzik 07 Oct '19

07 Oct '19

External Email - Use Caution Hi Doug, I would like to test whether an effect that I observed in a given voxel is larger than in other voxels (this is fMRI data). The additional complication is that I would like to stick as close as possible to the original analysis that yielded these effects, which were fixed effects. I am wondering whether that is somehow possible using selxavg3 and mri_glmfit? Thank you! Caspar

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