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30070 discussions

Request for password to unzip pre-installed VM freesurfer.
by Nathan Santana Schunk 08 May '23

08 May '23

External Email - Use Caution Hi, could anyone inform me what is the the pass code needed to unzip the FS_7_2_0_Ubuntu_18_04_06.ova.7z archive? I requested it a few days ago but got no response, so I'm asking once again in case my message got somehow unnoticed. (P.S.: I also checked the email spam tab). Thanks.

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mris_register options
by Koten, Jan Willem (jan.koten＠uni-graz.at) 08 May '23

08 May '23

External Email - Use Caution Dear Doug Dear Bruce Martin Reuter suggested me to write you since you are familiar with true inner workings of free surfer. In my project I try to create a family specific template that is based on three or more family members. We try to avoid the bias that may arise by choosing one family member as a target. There is procedure that tries to this described in: https://secure-web.cisco.com/1Blsa_5fBePXLqTD4MyXB0MVZ8BfrqXwEgfuiFRtv-42VQ… We found out that family specific templates result in better alignment among family members when compared to the standard fs average template. The creation of a template depends on the mris_register command that has several options that can be manipulated. However, we do not know what those options are doing in detail What is the initial sulcal alignment? Is this a rigid alignment procedure? Maybe a hard spherical rotation based on least squares algorithms? What is the final curve alignment? Is this a non-linear alignment procedure? If sulcal alignment is rigid, why does it take three times as long as non-linear curv alignment? What is normalization in context of mris_register which can be disabled trough the -nonorm step? Does the spring factor affect how much the Individual scul/curv maps are aligned with the family template? And if the latter is the case what is a reasonable spring value if you want to obtain individuals that are as closely matched to the family template as possible? Thank you in Advance Many greetings from Austria Jan

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Hemisphere Volume
by Necati Emre Şahin 08 May '23

08 May '23

External Email - Use Caution Dear FreeSurfer administrator *I hope everything is alright. I want to get some help from you.* I'm using FreeSurfer version 7.2.0. I want to obtain the total volumes of the left and right hemispheres separately. However, I could not see this information in any stats file. How can I see directly or calculate indirectly? Best regards, Necati.

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PETsurfer: PVC without psf of the scanner
by Federica Di Antonio 08 May '23

08 May '23

External Email - Use Caution Dear experts, Few weeks ago i wrote to this mailing list but I didn't receive any answer, so I'll try again: mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz --default-seg-merge --auto-mask 1 .01 --mgx .01 --o gtmpvc.output If I put psf to 0, there is no PVC, and the same happens if I don’t put that flag at all.t all Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user? I apologize for the repetition, Thanks for your patience, Federica

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error with mri_convert from nii made from TIFFs
by Andrew M 08 May '23

08 May '23

External Email - Use Caution I have a head CT comprised of 186 .tiff files from the original study. I converted these files to .nii by using MRIcroGL's TIFF->DICOM converter, and now tried using mri_convert -rl to get it into fs space. However, I get the errors: error: No such file or directory error: niiRead(): unsupported datatype 2304 (with scl_slope = 0) in /Users/andrewmichalak/Desktop/RNS/CURNS8/Imaging/CURNS8_post_CT.nii Is there a different method to convert TIFFs (or PNG, JPEG, etc.) to DICOM or .nii for use in the freesurfer ecosystem? Thank you!! -- Andrew

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Coordinates of Tracula clusters
by Makenna B McGill 05 May '23

05 May '23

External Email - Use Caution Hi Freesurfer Developers, I'm conducting along-tract statistics using trac-all -stat and mri_glmfit-sim in FS v7.3.2, and I'm hoping to produce coordinates of where significant clusters are located along the mean tracts in template space. I've attached an example of my cluster summary txt files and have two questions: 1) Is it expected that this analysis would produce voxel indices for the output file (e.g., VoxX) rather than coordinates? 2) If so, what might be the best way to report coordinates in template space? I've overlaid the statistical outputs on the template tracts for visualization in freeview as described at the end of the Tracula tutorial ( https://secure-web.cisco.com/168WgBh44N5UFj4ozgWFlHSW0vhEupgM52Ka0yY-taK9tN…) but I'm wondering if there is a more efficient and exact way to determine coordinates of these clusters along the template tracts. Thank you for any clarification you can provide. Best, Makenna *Makenna McGill *(she/her) Doctoral Student in Clinical Psychology The University of Texas at Austin

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freeview surface edgecolor overlay
by Dr. Cornelius Kronlage 05 May '23

05 May '23

External Email - Use Caution Dear freesurfer team, in freeview, setting surface edgecolor in axial/saggital/coronal slices to the overlay color seems to have stopped working between 7.1.1 and 7.2.0 (and up until 7.3.2). This might have been fixed in the development version meanwhile, but I couldn't find anything on the list. To reproduce: >recon-all --version freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551 >cd $SUBJECTS_DIR >freeview -f fsaverage/surf/lh.pial:overlay=fsaverage/surf/lh.thickness:edgecolor=overlay --viewport axial ># edge color is color according to overlay data as expected >recon-all --version freesurfer-linux-centos8_x86_64-7.2.0-20210720-aa8f76b >cd $SUBJECTS_DIR >freeview -f fsaverage/surf/lh.pial:overlay=fsaverage/surf/lh.thickness:edgecolor=overlay --viewport axial ># edge color is black Best wishes Cornelius

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control.dat not working
by Rosalia Dacosta Aguayo 05 May '23

05 May '23

External Email - Use Caution Dear Freesurfer subjects, After saving my control.dat file into the tmp folder and running the command line recon-all -autorecon2-cp -autorecon3 -s.... It does not seem to parse the control.dat file correctly and find the control points. This is what I get (in recon-all.log): #@# Intensity Normalization2 Fri 5 May 08:01:43 CEST 2023 /home/rosalia/Desktop/CAN_RUTI/sub-041_ses-FU1/mri mri_normalize -seed 1234 -f /home/rosalia/Desktop/CAN_RUTI/sub-041_ses-FU1/tmp/control.dat -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz /bin/tcsh: /home/rosalia/software/fsl/fslpython/lib/libtinfo.so.6: no version information available (required by /bin/tcsh) setting seed for random number genererator to 1234 using control points from file /home/rosalia/Desktop/CAN_RUTI/sub-041_ses-FU1/tmp/control.dat... assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading mri_src from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... Reading 0 control points... Doing gentle normalization with control points/label error: No such file or directory error: MRI3dGentleNormalize: mean = 0.0, nctrl = 0, norm failed Interestingly, when I saved the control points, freeview offered saving it as control.json, and the content of control.dat is, indeed, follows the JSON format. I renamed the file to control.dat (as in the tutorial). Is it possible that I should have kept it as control.json? P.S.: There is also a typo in the log. "random number genererator" should be "random number generator". :) Kind regards, Rosalia

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freeview rh and lh overlay_mask files both showing in the lh hemisphere
by Jewelia Karina Yao 05 May '23

05 May '23

External Email - Use Caution Hi FreeSurfer Developers, I'm trying to use freeview to load the rh and lh inflated surfaces together with overlays and overlay masks. I'm able to this separately and successfully for each hemisphere, but when I try to load the hemispheres together, both of the overlay_mask files show up on the left hemisphere and not the right hemisphere. The following is the command I'm using: freeview -f ${SUBJECTS_DIR}/${SUBJECT}/surf/rh.inflated:curvature_method=binary:overlay=rh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/rh.ve_20pct.thresh.label \ -f ${SUBJECTS_DIR}/${SUBJECT}/surf/lh.inflated:curvature_method=binary:overlay=lh.phase.mgz:overlay_custom=1.57,153,0,0,2.20,255,0,0,2.83,255,255,0,3.46,0,255,255,4.08,0,0,255,4.71,0,0,102:overlay_threshold=1.57,4.71:overlay_color='clearlower','clearhigher',colorscale:overlay_mask=${SUBJECTS_DIR}/${SUBJECT}/label/lh.ve_20pct.thresh.label I've tried running this with 7.1.1 and 7.2.0 on Mac 10.15.7 and Linux w/Ubuntu 22.04 but still run into the same issue. Let me know if there's something I'm missing or if there's a better way to troubleshoot. Thanks! Jewelia

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Why is this happening?
by Rosalia Dacosta Aguayo 05 May '23

05 May '23

External Email - Use Caution Dear Freesurfer's experts, Why is this happening? Kind regards, Rosie

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