[Freesurfer] Freeview - hide coordinate labels in scripts for screenshots {Disarmed}

External Email - Use Caution Freesurfer people, Is there an option for freeview scripts to hide the coordinate labels in 2D view? They are appearing in screenshots and I want to get rid of them. Chris. Dr Chris Adamson Senior Research Officer, Developmental Imaging, Clinical Sc

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Re: [Freesurfer] Freeview - hide coordinate labels in scripts for screenshots {Disarmed}

Hi Chris, Within the File menu of freeview, there will be a 'save screenshot as' button where you will be given the option of hiding the cursor, coordinates, and scale bar. Hope that helps, Jocelyn From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Chri

Re: [Freesurfer] mris_pmake error - freadFloat: fread failed

Can you open the smoothwm with another application? Eg, mris_info or freeview -f On 11/12/2020 9:52 AM, Nasr, Shahin,Ph.D. wrote: Hi Surfers,      For one subject, when I run mris_pmake as below: mris_pmake --subject --hemi lh --surface smoothwm --mpmProg pathFind --mpmArgs vertexStart:,vert

Re: [Freesurfer] AAL Segmentation with Freesurfer

run recon-all on the AAL anatomical T1w volume template On 11/12/2020 1:52 PM, Stephan Wunderlich wrote: > External Email - Use Caution > > Dear all, > > Is there a possibility to segment a brain with freesurfer to an AAL Atlas. So > that I get the volume and amount of voxel for all the

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

sorry, I don't know what you are asking On 11/12/2020 8:30 PM, 李梦君 wrote: External Email - Use Caution Thanks! I get only one area value in the lh_areapial.sum file with this command: mri_segstats --i qdec/Areapial_15_L/y.mgh --slabel fsaverage lh lh.areapial.label --avgwf lh_areapi

Re: [Freesurfer] eddy_correct with DTI {Disarmed}

What version of FSL are you using? On 11/10/2020 12:19 AM, Wei Shao wrote: External Email - Use Caution Hi, Freesurfer team, My name is Weishao, Here is a problem that bothers me a lot I try to run DTI. I have loaded the FSL module and use the most recent version of Freesurfer. it's

Re: [Freesurfer] mris_pmake error - freadFloat: fread failed

Good morning Doug, I can load ?h.white and rh.smoothwm but not lh.smoothwm to freeview. I can even load lh.smoothwm.nofix. So apparently, that is the corrupted file. So, would you tell me how to regenerate the lh.smoothwm without redoing the whole recon? Thanks __

Re: [Freesurfer] tkregister issue with reg-feat2anat

External Email - Use Caution Not presently, as I would need to install on my personal computer. I can ask HPC IT to replace the file again and retest to see if things replicate... Erin From: Douglas N. Greve Sent: Friday, November 13, 2020 11:4

Re: [Freesurfer] tkregister issue with reg-feat2anat

I'm sure they will. When you re-run it, add --debug as the first argument and capture the entire terminal output to a file (don't try to take a snapshot) On 11/13/2020 11:50 AM, Walsh, Erin wrote: External Email - Use Caution Not presently, as I would need to install on my personal c

Re: [Freesurfer] Sulc maps

External Email - Use Caution I should have mentioned that the HCP data have been processed using FS5.3HCP. If we know which code/script generates sulc files, we can try to dig out the code to find the scaling factor. On Thu, Nov 12, 2020 at 9:46 PM Reza Rajimehr wrote: > Thanks

Re: [Freesurfer] eddy_correct with DTI {Disarmed}

External Email - Use Caution Hi Douglas I think it's 5.0.11 [weishao@gra-login2 ~]$ module load nixpkgs/16.09 freesurfer/7.1.0 To initialize FreeSurfer, do (sh, ash, ksh, and bash) source $EBROOTFREESURFER/FreeSurferEnv.sh or (csh, tcsh) $EBROOTFREESUR

Re: [Freesurfer] tkregister issue with reg-feat2anat

External Email - Use Caution Thanks. I have attached the error output when using the debug option when attempting to run a subject. When I type from the command line (no --feat or --subject options), it is an identical error: [edub@longleaf-login1 Freesurfer]$ reg-feat2anat --d

[Freesurfer] Problem with volumes of hypothalamic segmentation

Dear all, We have found a problem with the volumes of the hypothalamic units in our recently released volume, which we are working to fix ASAP. So, just to be clear the segmentations are fine, but the estimations of the volumes of the nuclei (i.e., the CSV files) are not. Apologies for any inconv