[Freesurfer] Error with "recon-all -make all" following multiple manual editing

External Email - Use Caution Dear Freesurfer's experts, Havng done multiple types of manual editing in two subjects, I relaunched the recon-all process (Freesurfer 6.0.1) with the flag "-make all". However, during the process, I goth for both subjects the following error mess

[Freesurfer] (no subject)

External Email - Use Caution Hi FS experts, I use tksurfer (e.g., tksurfer fsaverage/ lh inflated -gray) to open the overlays (i.e., something.sig.cluster.mgh) I generated with the permutation simulation correction. It goes perfectly well for most of them expect for some, where t

Re: [Freesurfer] nu_correct: Command not found

External Email - Use Caution Could you replace this line: export PATH=/usr/local/freesurfer/bin:PATH=/usr/local/freesurfer/mni/bin:$PATH with this one and try again: export PATH=/usr/local/freesurfer/bin:/usr/local/freesurfer/mni/bin:$PATH Please also paste the output of th

Re: [Freesurfer] Group X Time Interaction in Qdec

There is not a way to do this. Instead, try a paired analysis https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis On 3/28/19 8:08 PM, brain health wrote: External Email - Use Caution What is the best way to run a whole- brain Group (intervention group, control group) x Time (Pre, p

Re: [Freesurfer] (no subject)

What threshold are you using in tksurfer? It should be the same as -log10(cwp), where cwp is the --cwp threshold you used in mri_glmfit-sim. If it is different, then it might not show all the cluster On 3/29/19 6:48 AM, Giuliana Klencklen wrote: External Email - Use Caution Hi FS exper

Re: [Freesurfer] VT images from pmod to freesurfer

what program generated the error? What is the full command line for that program? On 3/21/19 12:49 PM, Donatienne Van Weehaeghe wrote: External Email - Use Caution Dear, I encountered a problem when going from pmod to freesurfer. I made Vt images in pmod using the logan plot, then I us

Re: [Freesurfer] VT images from pmod to freesurfer

External Email - Use Caution Dear, The Freesurfer program generated the error after multiple comparison corerction. Thank you for your help. Kind regards Donatienne Op vr 29 mrt. 2019 om 10:58 schreef Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu>: > what program generated

Re: [Freesurfer] mris_preproc not running

Can you send your full command line and the full terminal output? Are you sure you're using the new command? On 3/27/19 10:33 PM, Sims, Sara A (Campus) wrote: > External Email - Use Caution > > Doug, > I have implemented the new version of the command. I am getting this error > when I a

Re: [Freesurfer] VT images from pmod to freesurfer

What is the full command line for that program? On 3/29/19 11:01 AM, Donatienne Van Weehaeghe wrote: External Email - Use Caution Dear, The Freesurfer program generated the error after multiple comparison corerction. Thank you for your help. Kind regards Donatienne Op vr 29 mrt. 2019

Re: [Freesurfer] VT images from pmod to freesurfer

External Email - Use Caution #mri_glmfit --glmdir /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/PVC_proj0.5_lh --y /autofs/cluster/atassigp/Users/Donatienne/Analyses_freesurfer/recon_flair/VT/VT/concatenate/all.lh.mgx.ctxgm.fsaverage.pv

[Freesurfer] segmentHA_T1_long.sh HBT issue

External Email - Use Caution Hello, I have run *segmentHA_T1_long.sh from the developer freesurfer version and am looking to segment and visualize the head body and tail of the left and right hippocampus.* *However, when looking at the lh.hippoAmygLabels-T1.long.v21.HBT.FSvoxelS

[Freesurfer] petsurfer

External Email - Use Caution Hi developers,I am using the petsurfer now to do the PVC for my dynamic analysis, however there is something error happened. Here is my commends: mri_coreg --mov fICL161363_06_1_BU99008_9744_merged_00015.nii --ref fICL161363_06_1_MRI_9746_ser

[Freesurfer] segmentHA_T1_long.sh HBT issue

External Email - Use Caution Hello, To add to my original post it seems the issue is I am not able to look at these merged images or that the HBT file write out seems to be wrong? I don't know how to post a picture to the listserve so someone can determine if I am just looking at

Re: [Freesurfer] petsurfer

What is fICL161363_06_1_MRI_9746_series_2_MPRAGE_ADNI_P2.nii ? In general, you should not give mri_coreg a reference when using --s unless it is the same geometry as the orig.mgz On 3/29/19 11:55 AM, ?? wrote: External Email - Use Caution Hi developers, I am using the petsurfer now

Re: [Freesurfer] segmentHA_T1_long.sh HBT issue

External Email - Use Caution Dear Daniel, This is weird. Can you please send us lh.hippoAmygLabels-T1.long.v21.*.mgz for a sample subject? Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on b

[Freesurfer] Partial volume correction for aseg.mgz files

External Email - Use Caution Hello, I'm trying to extract regions (mri_extract_label) of interest from the aseg.mgz files and compare them to our manual segmentations. I've warped these ROI masks onto our native space. I've noticed on the forum that there were mentions of discr

[Freesurfer] segmentHA_T1_long.sh HBT issue

External Email - Use Caution The issue was that I was using the freesurfer 6.0 version of freeview and not the development version. Thanks for your help Eugenio! Best, *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science* Exercise for Brain Health Lab University of Mar

Re: [Freesurfer] Partial volume correction for aseg.mgz files

Hi Da-Yea you would need to compute the jacobian of the warping and apply it at each voxel to scale the volumes (accounting for the warping). cheers Bruce On Fri, 29 Mar 2019, Song, Da-Yea wrote: External Email - Use Caution Hello,   I’m trying to extract regions (mri_e