Freesurfer

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17 participants
30099 discussions

How to register the workshop at Boston
by Yun Wang 26 Jan '16

26 Jan '16

Dear All, I am new to Freesurfer, so I want to take the Freesurfer Workshops at Boston this April. But It appears I have passed the deadline to register. Does anyone know how to make it happen? Thanks! Yun Wang

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DESPOT T1 map
by Worker, Amanda 26 Jan '16

26 Jan '16

Hi All, I have a T1 map which has been synthesised from a DESPOT imaging sequence and I am hoping to use this as input to recon-all. Do you know if this will be possible at all, or if there is anything I can do to prepare the T1 map to run through recon-all? Thanks in advance, Amanda

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mri_aparc2aseg BA.annot
by Qiyuan Tian 26 Jan '16

26 Jan '16

Hi, I was trying to use mri_aparc2aseg to convert the BA.annot (or BA.thresh.annot) to segmentation volume, that will be then converted to EPI space for some diffusion data. I tried both the BA.annot for the individual subject as well as the PALS_B12_Brodmann.annot in fsaverage. The command line I used was: mri_aparc2aseg --s s1 --annot BA.annot --o BAseg.mgz. It seems that this command is working, but when I view the BAseg.mgz file in freeview, the index for the BA areas seems wrong. For example, for BA1, the index says 2004 for ctx-rh-corpuscallosum. It seems that the index for BA areas in FreeSurferColorLUT are from 400 to 414. Is there a way to make the index correct? Or mri_aparc2aseg can only be used for aparc.a2009s.annot or aparc.annot? Thanks a lot. Best QT

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Qdec ROI Analysis
by Larissa McKetton 26 Jan '16

26 Jan '16

Dear Freesurfer community, I am working on an ROI analysis using qdec. I have created all aseg and aparc stats files and would like to determine if there are any differences in volume, surface area, and thickness for certain structures between two groups. I was wondering with the analysis, would it be okay to use the resulting aseg/aparc output stats from either the Desikan/Destrieux atlases and run these values through SPSS or is it better to draw ROI labels on the fsaverage brain, apply the label to each subject, and run the analyses this way. I am asking because the following tutorial states: *"Note*: If you want to use a pre-existing label and register it to fsaverage, be aware that this might involve two instances of resampling and the results might not be as accurate as they would be if you drew the label on fsaverage. Please contact the FreeSurfer team to get more details on this process if you have any concerns." http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI#Tableofth… If drawing labels on the fsaverage brain and applying them to each subject is the way to go- would I need to correct for multiple comparisons? Many thanks, Larissa

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-hippocampal-subfields-T1 fails in freesurfer-Darwin-OSX-dev-20160109
by Carl Anderson 26 Jan '16

26 Jan '16

Hi Everyone, Subfields seems to fail to run when part of the recon-all -all command line and also fails when run on its own (but gives no error). Here is the output and recon-all log attached: Thanks! Carl Fitting mesh to synthetic image from ASEG took 468.3773 seconds Transforming points Transforming points dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin//../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/local/lib/libgcc_s.1.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/bin//../lib/gcc/lib/libgomp.1.dylib Expected in: /usr/local/lib/libgcc_s.1.dylib /bin/bash: line 1: 22256 Trace/BPT trap: 5 /Applications/freesurfer/bin//mri_convert tempT1.mgz T1resampled.mgz -odt float -rt cubic -vs 0.33333 0.33333 0.33333 > /dev/null /Applications/freesurfer/bin//mri_convert tempT1.mgz T1resampled.mgz -odt float -rt cubic -vs 0.33333 0.33333 0.33333 >/dev/null: Trace/breakpoint trap mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, -1): could not open file error reading from volume T1resampled.mgz threshold mask volume at 0.5 mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, -1): could not open file /Applications/freesurfer/bin//mri_mask: could not read source volume T1resampled.mgz /Applications/freesurfer/bin//mri_mask -T 0.5 T1resampled.mgz asegModBinDilatedResampled.mgz T1resampled.mgz >/dev/null: Signal 124 mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, -1): could not open file error reading from volume T1resampled.mgz mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/hippoMaskResampled.mgz, -1): could not open file threshold mask volume at 0.5 mghRead(/Applications/freesurfer/subjects/ParallelEveryone/CAT104/tmp/hippoSF_T1_v10_right/T1resampled.mgz, -1): could not open file /Applications/freesurfer/bin//mri_mask: could not read source volume T1resampled.mgz /Applications/freesurfer/bin//mri_mask -T 0.5 T1resampled.mgz hippoMaskResampledDilated.mgz T1resampled.mgz >/dev/null: Signal 124 Error using kvlAtlas3D_Matlab /autofs/space/panamint_005/users/iglesias/software/MAC_ATLAS_3D/Atlas3D_131025/itkMGHImageIO.cxx:216: itk::ERROR: MGHImageIO(0x103507280): Can't find/open file: T1resampled.mgz Error in kvlReadCroppedImage (line 11) Error in segmentSubjectT1_autoEstimateAlveusML (line 605) #------------------------------------------ Started at Tue Jan 26 09:17:04 EST 2016 Ended at Tue Jan 26 09:34:33 EST 2016 #@#%# recon-all-run-time-hours 0.291 recon-all -s CAT104 finished without error at Tue Jan 26 09:34:33 EST 2016 -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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Brain stem segmentation in Freesurfer 6 {Disarmed}
by Alshikho, Mohamad J. 26 Jan '16

26 Jan '16

Dear Freesurfers, After segmenting the brain stem using FS6 tools. I used Free view to visualize the final images. In Free view I opened "orig.mgz", "wmparc.mgz" and "brainstemSsLabels.v10.mgz" Then I tried to check the segmented structures by flipping the images. I noticed an overlap between Ventral DC ( left and right) and mid brain ( as an output of brain stem segmentation). I "wmparc.mgz" atlas: Ventral DC and brain stem are totally different segments. Now After segmenting the brain stem. I see that the Ventral DC belongs to the mid brain. Is this natural? Thanks in advance for any suggestion! Mohamad

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Incomplete output
by maryam koochaki 26 Jan '16

26 Jan '16

Dear experts,I am kind of new at working with freesurfer.recon-all process has completed without error, but when I look at brainmask volume on freeview, one of the issues is that lateral ventricle is completely excluded. I have tried to edit it with editing the white matter volume, but no success so far. I do not know how to correct it. Have anybody here had the same issue? Thanks,Maryam

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Centroid of a binary volume question
by pfotiad＠nmr.mgh.harvard.edu 25 Jan '16

25 Jan '16

Dear FS Community, I was wondering whether there is a way to create a binary volumetric file of just the centroid of a binary volume (represented maybe as a dot of 1x1x1 mm^3 voxel size). I know how to find the coordinates of the centroid (through either the fslstats command or MATLAB), but I didn't know whether there was a way to create a new binary volume of just the centroid through the terminal. (I would do it manually, but I have ~500 binary volumes that I would like to apply the same method to). Thank you in advance for your help! Best, Panos

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separate non-contiguous labels
by dgw 25 Jan '16

25 Jan '16

Hi, I want to separate each label in the Yeo parcellations into each of their separate contiguous labels. Is there a command, which can do this in Freesurfer? Example lh.yeo7.annot the network 7 label has 5 non-contiguous components Is there a command to separate these into 5 separate labels? Thank You, Dan

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Brainstem segmentations (6.0)
by Cat Chong 25 Jan '16

25 Jan '16

Hello Experts, We used the brainstem segmentation that is built into FS 6.0, to interrogate midbrain volumes. My question was: the way FS segments the midbrain, does it include the cerebral peduncles? cheers,Cat

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