Re: [Freesurfer] recon-all-rms error < 2.00

can you send us the recon-all.log file (as a text file)? On Thu, 7 May 2020, jiahui wrote: External Email - Use Caution Hello FreeSurfer Developers, I run the recon-all -all command: this true error?how to resolve this problem? ERROR: 245/300: dt: 0.9000, rms radial 

[Freesurfer] recon-all-rms error < 2.00

External Email - Use Caution Hello FreeSurfer Developers, I run the recon-all -all command:this true error?how to resolve this problem? ERROR: 245/300: dt: 0.9000, rms radial error=134. 782, avgs=0 250/300: dt: 0.9000, rms radial error=134. 022, avgs=0 255/300: dt: 0.9000, rms

Re: [Freesurfer] Recon-all exited WITH errors

It looks like that command finished without error. Have you tried running it in recon-all again to see if it fails again? You can just run that command with -parcstats3 On 5/6/2020 6:41 AM, Mason Wells wrote: External Email - Use Caution Hi Doug, Not sure if my email below got to

Re: [Freesurfer] Get Atlas surfaces in subject space

That looks like it could be right. It has 102,020 vertices, which should be the number of vertices in the target subject (and is in the typical range for an individual subject) On 5/6/2020 10:21 AM, Ian Hardingham wrote: External Email - Use Caution FSLInfo attached, thanks Bruce.

Re: [Freesurfer] mean for a bash script from mris_calc.

So you want a mean over all the vertices? The easiest thing to do is something like mri_segstats --i surf.overlay.mgh --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --id 1 --avgwf mean.dat mean.dat will have a single number that will be the mean over the cortex label. On

Re: [Freesurfer] Hippocampus Subfields Segmentation

The file with HBT in the name. See https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala On 5/6/2020 2:14 PM, Muhammad Naveed Iqbal Qureshi wrote: External Email - Use Caution Hi FreeSurfer experts, I preprocess my data with FreeSurfer v 6. After it I ran

[Freesurfer] freesurfer 7.0.0 in a virtual machine...

External Email - Use Caution Hi: How can install freesurfer 7.0.0 in a virtual machine ? Sincerely, Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] mean for a bash script from mris_calc.

External Email - Use Caution I am trying to calculate the mean for a surface mgh file and use the standard deviation to adjust the range when I make tiff file from the beta from a lme model. I wish to store the result in a bash variable. > On 6 May 2020, at 19:56, Douglas N.

Re: [Freesurfer] Get Atlas surfaces in subject space

External Email - Use Caution FSLInfo attached, thanks Bruce. When trying to run freeview I get "freeview.bin: error while loading shared libraries: libpng12.so.0: cannot open shared object file: No such file or directory" - do I need to add /usr/local/freesurfer/lib/* to path

[Freesurfer] Hippocampus Subfields Segmentation

External Email - Use Caution Hi FreeSurfer experts, I preprocess my data with FreeSurfer v 6. After it I ran developmental version of freesurfer to get the hippocampus subfields ROI and volume. I get the following output: # Hippocampal subfield volumes as created by

Re: [Freesurfer] mean for a bash script from mris_calc.

Are you trying to compute the mean at each voxel? Try mri_concat file.mgz --mean --o file.mean.mgz Assuming that file.mgz has multiple frames. If you have each input in a separate file, you can just mri_concat file1.mgz file2.mgz ... --mean mean.mgz To compute the stddev, use --std instead of

[Freesurfer] mean for a bash script from mris_calc.

External Email - Use Caution Dear Freesurfer experts, I have tried to use mris_calc to calculate mean and std and export the variable to bash with this command, mean=$(mris_calc mghfile std), but the array is not stored in mean. Is there any other way to calculate, mean and

Re: [Freesurfer] T1 recon -all error "XL defect detected"

Qi, in this context a "defect" is not just a place where the surface is inaccurate. It is a place where the surface is topologically incorrect, ie, a "handle" or a "hole" in the surface. Such defects are quite common and usually fixed by recon-all automatically. Sometimes the defects can be

Re: [Freesurfer] T1 recon -all error "XL defect detected"

ok, now I'm confused. Did recon-all finish or is it still running? What does the end of the recon-all.log file say? Note that the spatial location of the inflated surfaces relative to the volumes doesn't mean anything cheers Bruce On Wed, 6 May 2020, Zeng, Qi wrote: External

Re: [Freesurfer] stats t test

yes On 5/5/2020 7:16 PM, jiahui wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute gray matter volume average thickness.Can I use them from stats file to compare two groups (HC and diesease) through t test? 1) FreeSurfer version:

Re: [Freesurfer] Get Atlas surfaces in subject space

sorry, I'm going to defer to Doug on surf2surf On Wed, 6 May 2020, Ian Hardingham wrote: External Email - Use Caution Thanks Bruce. So a reminder I'm calling: mri_surf2surf --hemi lh --srcsubject fsaverage --sval-xyz white --trgsubject fs_target --tval-xyz

Re: [Freesurfer] recon-all-rms error < 2.00

please don't send text files as images! We can't search them, etc... The final distance error sis not a problem. Does recon-all stop? Please send the recon-all.log as a text file cheers Bruce On Tue, 5 May 2020, jiahui wrote: External Email - Use Caution Hello FreeSurfer

Re: [Freesurfer] Get Atlas surfaces in subject space

hmm, that is not an icosahedral surface, which should have 160K vertices. Can you check your input surface? You'll also need to fix your freeview problem, but someone else will have to help you with that On Wed, 6 May 2020, Ian Hardingham wrote: External Email - Use Caution

Re: [Freesurfer] T1 recon -all error "XL defect detected"

Hi Qi it is not obvious from that one image that something is wrong there. What does a saggital view look like with the cursor on that region? Also, can you send an image of the rh.inflated.nofix in 3D mode? Sometime XL defects are fixable automatically, which may be the case for your

Re: [Freesurfer] Get Atlas surfaces in subject space

can you run mris_info on the output surfcae? And maybe send a freeview snapshot of it (in 3d rendering mode) On Wed, 6 May 2020, Ian wrote: External Email - Use Caution Thanks Tim and Doug. I have the files generating and loading properly now, but I'm not convinced it's giving the

Re: [Freesurfer] Get Atlas surfaces in subject space

External Email - Use Caution Thanks Tim and Doug. I have the files generating and loading properly now, but I'm not convinced it's giving the output I'm looking for. I am trying to convert the "fsaverage" subject's surface coordinates to my own subject's surface space.

Re: [Freesurfer] Recon-all exited WITH errors

External Email - Use Caution Hi Doug, Not sure if my email below got to you? I sent the terminal outputs of the command you told me to run. Any idea what’s going on or how to fix it? Cheers, Mason Mason T Wells, MSc PhD student School of Optometry and Vision Sciences & Cardiff

Re: [Freesurfer] Get Atlas surfaces in subject space

External Email - Use Caution Just a note: there should be no need to convert to gifti, nibabel can read the FreeSurer binary surface format directly with `nibabel.freesurfer.io.read_geometry()`. The docs are here: