[Freesurfer] area.pial files for fsaverage

External Email - Use Caution Dear FS developers, I have noticed that for each subject, there are ?h.area and ?h.area.pial files under the $SUBJECT_DIR/$subject/surf sub-directory. According to Bruce's words from here https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg2

Re: [Freesurfer] mri_fieldsign error

External Email - Use Caution I tried on our Linux: Centos Linux 7 (core), ID_like = ‘rhel fedora’ with the same “segmentation fault (core dumped)” error. Thanks, Xiaomin From: Xiaomin Yue Sent: Friday, July 17, 2020 6:07 PM To: Freesurfer support list<

[Freesurfer] outlier detection and remove

External Email - Use Caution Hi, I have a question about how to handle outliers in aparc, aseg and tracula results? Usually, each subject has one result regarding one measurement and I detect and remove outliers using barplot. However, for results in freesurfer, we have multiple o

Re: [Freesurfer] How to do permutation for multiple comparison correction?

External Email - Use Caution Hi Doug, For your questions: 1. "Not sure what you mean by in the ROI. Are you trying to permute across space? That generally does not work because the points are not exchangeable across space." By "In the ROI", I mean for all vertices listed in t

Re: [Freesurfer] PETSurfer questions - Part II

On 7/20/2020 2:56 AM, Ferraro, Pilar wrote: External Email - Use Caution Many thanks for the reply, Yep, unfortunately MG values are always much higher than SGTM ones (in all the ROIs). I wonder whether this might be related (for MG and MZ) to the absence of a normalization using t

Re: [Freesurfer] Fwd: Cortical Parcellations in FreeDurger 7

I don't know. I'm not that familiar with FSL programs. If you want our help, try using mri_segstats. If something goes wrong send the command line On 7/21/2020 10:26 AM, Al Qadi, Ameen wrote: External Email - Use Caution Hi Douglas, I see the CLUT file, it's the same one I've been us

Re: [Freesurfer] recon all Freesurfer 7.1 on Mac High Sierra fails to run for some subjects

This is a known problem with mri_cc on Mac. Any day now we will release 7.1.1 that will include a patch to fix this. On 7/21/2020 7:05 AM, Annelies Vant Westeinde wrote: External Email - Use Caution Hi, I am attaching some recon-all log files as requested (hope it works like that).

Re: [Freesurfer] How to do permutation for multiple comparison correction?

On 7/21/2020 1:12 AM, Xiaojiang Yang wrote: External Email - Use Caution Dear FS experts, Instead of using mri_glmfit-sim, I am trying to implement a customized multiple comparison correction algorithm using permutation. Before I implement my own, I want to make sure my permutation

[Freesurfer] Fwd: Cortical Parcellations in FreeDurger 7

External Email - Use Caution Hi Douglas, I see the CLUT file, it's the same one I've been using. I have been using FSL (fslmaths) to extract anatomical ROIs from the aparc+aseg using the CLUT indices as thresholds. This normally works, but results in empty ROIs for thalamic nuclei

Re: [Freesurfer] error in longitudinal stream fs7.1 ERROR: Number of filenames for --iscalein should agree with number of init LTAs (--ixforms)! worked in fs6

Yep, I just found that error yesterday. I put a new longmc script in that same location with another fix -- but I have not fully tested it yet:) On 7/21/2020 1:12 AM, Knut J Bjuland wrote: External Email - Use Caution Thanks it worked for subjects with more than one timepoint but when

Re: [Freesurfer] FsAverage4 vertex coordinates

Use mris_convert to convert the white or pial surfaces to ascii On 7/20/2020 3:41 PM, Walsh, Shane W. wrote: Hi FreeSurfer developers, I'm looking for the xyz coordinate table for the vertices of the FsAverage4 atlas. I have fMRI data that has been sampled to the FsAverage4 space and it would

Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

To answer #2, You should definitely not mix them. For #1, the study has not been done. In principle, FLAIR is better because T2 has both bright and dark in the extra cerebrum whereas FLAIR has only dark. That said, there might be other factors that could make FLAIR worse. On 7/20/2020 12:13 PM

Re: [Freesurfer] Flag(s) for parallel processing

No, I don't think that 3 hour number was ever accurate. On 7/20/2020 10:12 AM, Billah, Tashrif wrote: Hi Douglas, You asked a good question which prompted me to do an experiment with just "-threads 8 -itkthreads 8". The run time has been quite slower (~8 hours) compared to ~5 hours it took wit