Re: [Freesurfer] Error during skullstripping: numerical result out of range

External Email - Use Caution Hello experts, So I did not see brainmask.mgz in mri folder and it looked like reconall stopped at mri_em_register stage because I couldn't find talairach_with_skull.lt in transforms folder. So I tried running mri_em_register again and got the followi

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

External Email - Use Caution Hi Anastasia Thanks so much- I think I got the error due to the format of the bvecs and bvals Trac-all is running but for one person it is running for almost 5 days now- I assume that can't be normal? It says 8/18 tracts are completed but these iterat

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed}

I think the reason for this may be that the data in fsaverage space (after mris_preproc) will have had a jacobian correction which will not be in data on the native surface. For this reason, I would not use #1. #2 is fine.You can apply your label in fsaverage space to the y.mgh used as input to

Re: [Freesurfer] Issue with tkregister command

Please remember to post to the list ... Can you run it with --debug as the first option, then post all of the terminal output? On 10/28/2020 11:21 PM, Elisabetta Ambron wrote: External Email - Use Caution Dear Prof Greve I am  having an issue running reg-feat2anat and I get the follo

Re: [Freesurfer] resolution greater than 1 mm segmentation

In version 7, just use --hires On 10/28/2020 11:53 PM, Gonzalo Rojas Costa wrote: External Email - Use Caution Hi:   I know that using an mprage image with greater than 1 mm resolution, freesurfer converts it to 1 mm previous segmentation. There is any option that freesurfer uses t

Re: [Freesurfer] Error in QDEC

sorry, we are not supporting qdec anymore. Please use the command line tools (mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim). See the tutorials On 10/16/2020 6:14 AM, Koustav Chatterjee wrote: External Email - Use Caution Hello, I have found the following error while click

[Freesurfer] BIDS-ASL request for comments - closes on Friday (Nov 13th) {Disarmed}

External Email - Use Caution The BIDS community is preparing to merge the ASL (Arterial Spin Labeling) extension. The updated draft is available for review at: https://secure-web.cisco.com/1t4ZzOsfsvFPLRNF1xylkG0C9rf6FgtaTu4o9Dl7kHsW-tzrZVgK77RfeUpAcEoMP4o6RRVZ4R45vZr_1JxxHGxb4zc

[Freesurfer] mri_glmfit_sim error

External Email - Use Caution Hi all, I ran a multiple comparison correction for a surface based analysis with this command: mri_glmfit-sim --glmdir rh.project.glmdir --cache 2 abs --cwpvalthresh .05 --2spaces But I am getting the following error: cannot find /usr/local/freesu

[Freesurfer] mri_convert error

External Email - Use Caution Dear Freesurfer Developers, Apologies for double posting. I am attempting to convert some dicom files to mgz via mri_convert command. However, for only 5 participants from my cohort I get the following error. Could you please help me to resolve the pro

[Freesurfer] mri_convert error

External Email - Use Caution Dear Freesurfer Developers, I am sorry I did not include the error message. I am attempting to convert some dicom files to mgz via mri_convert command. However, for only 5 participants from my cohort I get the following error. Could you please help me

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed}

External Email - Use Caution Thank you very much! I tried to extract the areas with the following codes: mri_segstats --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec) --slabel lh.areapial.label (This was the label extracted from the fsaverage after multi-correction)

Re: [Freesurfer] trac-preproc error

Hi Yasemin - If you upload all the tracula output files for me here, I'll take a look: https://gate.nmr.mgh.harvard.edu/filedrop2/ Please include all the output directories for this one subject in one zip file. Thanks! Anastasia. From: freesurfer-boun...@nmr.mgh

Re: [Freesurfer] Tracula error

Hi Michele - Do you get any other output on the screen? Can you attach your configuration file and trac-all.log? Thanks! Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Michele Valotti Sent: Friday, October 30, 2020 12:44 PM To: Freesurfer

Re: [Freesurfer] Tracula error: run list is longer than subject list {Disarmed}

Hi Oshadi - That does not sound normal. Is there anything wrong with the FreeSurfer segmentation of this subject? Anastasia. From: Shanika Jayakody Sent: Monday, November 2, 2020 10:33 AM To: Freesurfer support list ; Yendiki, Anastasia Subject: Re: [Freesurfer