Freesurfer

freesurfer@nmr.mgh.harvard.edu

14 participants
30083 discussions

Global and lobar gyrification index
by K. Wagstyl 03 May '16

03 May '16

Hi all, Is there a way to calculate total hemispheric and lobar values of gyrification index? Either through a freesurfer-based command or through calculating the convex hull areas independently? We've thought about averaging local gyrification index for the hemisphere but think that direct calculation is probably more appropriate. Thanks, Konrad

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Cortical Parcellation
by Heidi Foo 02 May '16

02 May '16

Dear FreeSurfer Experts, I am currently trying to run cortical parcellation on my subjects. However, I am getting error messages that the --outdir is unknown. This is the command I ran *mri_annotation2label --s FS_PD002_1.nii --hemi lh --lobesStrict --outdir ./label* Is there a way I can resolve this issue? Thank you so much for your kind attention. Best Regards, Heidi Foo

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import ROI analysis results from Matlab into FreeSurfer
by Domenico Zacà 02 May '16

02 May '16

Dear FS experts, I dumped the average cortical thickness values of 68 ROI using aparcstats2table into a spreadsheet, then generated a set of CT networks measures in matlab for each ROI. Now how can I visualize the results back in FreeSurfer? Thanks Domenico Zacà, PhD MR Lab Research Fellow Center for Mind/Brain Sciences University of Trento, Italy Via delle Regole, 101 38100 Mattarello (TN) Italy Telephone: +39-0461-28 3069 Fax: +39-0461-28-3066 Email: domenico.zaca(a)unitn.it MRI Methods Group: http://r.unitn.it/en/cimec/mri

2 1

Reg: Failed to load MRI
by Jesu Kiran Jk 02 May '16

02 May '16

Dear Freesurfer Experts, I wish to load wm.mgz, brain.mgz volumes with freeview. But it is giving me an error 'Failed to load MRI'. Why is it giving me this error and how could I correct this? Please help. Kind Regards, Jesu

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Command for generating spherical surface
by Muhammad Razib 02 May '16

02 May '16

Hi, I have some (freesurfer generated) pial surfaces, but I don't have the sphere surfaces of these. Is there a command in freesurfer to generate .sphere file from .pial file? --- Muhammad Razib

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question about FA display
by Zeng, Qi 02 May '16

02 May '16

Hi all, I got a question for FA display. I run recon-all without error, also no error with dt_recon, mri_vol2vol. I manually checked WM on T1 before displayed FA. Comparing with normal FA display, my FA was out of brain skull. What could the possible problem be during the process? Anyone can help. Thanks in advance ! Here attached the manual checking and FA display (comparing with normal FA) Best, Qi

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registration of intraparietal sulcus
by Bastian Cheng 02 May '16

02 May '16

Dear all, I am creating a hand-drawn label of the Intraparietal sulcus on fsaverge. When I register it to an individual brain (mri_label2label), the area is incorrectly registered and comprises adjacent brain structures that I am not interested in analyzing (specially the neighboring sulci). I know that registration works with my data in general, since other regions (manually drawn on fsaverage, i.e. various pre-motor areas) are correctly registered. is there any bias or "reduced" accuracy when registering regions of interest located at the parietal cortex? I am aware that aparc2009 comprises an area called "S_inrapriet_and_P_trans", but I've found that this label is not restricted to the sulcus (in individual segmentations). Any help would be appreciated!

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Tracula: a single curve for some tracts
by Xiaofu 01 May '16

01 May '16

Dear Anastasia, One quick question. I have run Tracula and found there was only one single curve for some tracts. But other tract went well I tried setting reinit parameter to 1 and rerunning "trac-all -prior" and "trac-all -path" but didn't get improved, e.g., the right UNC was a single curve (see attached). I also checked the initial seeds of right UNC (i.e.,endpt1.pd.nii.gz and endpt2.pd.nii.gz) and found those seeds were visually not correct when loaded to FA image. I guess maybe the reason of the single curve problem. Is there anyway to fix this problem? Looking forward to hearing from you. Thank you very much. Best, Xiaofu

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Recon-all -subcortseg finished with error
by Taha Abdullah 01 May '16

01 May '16

Hello All, I am running an analysis strictly on subcortical volumes, and to save time and disk space I wanted to avoid if possible construction of surfaces and seems that it is necessary? I first ran recon-all -autorecon1, second I ran recon-all -subcortseg and the final error was regarding no such file or dir, specifically the /surf/lh.white. Is there a better way to run this type of analysis to save disk space and time? Possibly using -autorecon2'; would love any input. Thank you in advance! -- Taha Abdullah Department of Physiology Northwestern University Masters of Science Physiology and Biophysics, Georgetown University 2015

2 4

Editing brain.finalsurfs.mgz
by maryam koochaki 29 Apr '16

29 Apr '16

Dear experts,I am trying to fix the surfaces which are crossing to each other in the middle where the hemispheres reach each other.As Bruce mentioned before I am trying to create two volumes (lh.brain.finalsurfs.mgz , rh.brain.finalsurfs.mgz ) nad edit them individually.Then I want to rerun this command for each hemi:mris_make_surfaces -subjid <name> -whiteonly -noaparc -mgz -T1 lh.brain.finalsurfs lh mris_make_surfaces -subjid <name> -white NOWRITE -mgz -T1 lh.brain.finalsurfs lh Am I using the correct command?What should I expect to have after running this command line(for example first one)?Sould I rerun (recon-all -autorecon-pial ) after all? Thanks in advance for the help, Maryam

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