Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

Freesurfer with infarct patients
by Budge, Mariana 03 Sep '17

03 Sep '17

Hi Freesurfer experts, I am running FS on a patient with a chronic right occipital lobe infarct as part of a larger study. The program does not recognize the area around the lesion as brain matter, and I am wondering how best to treat this situation. I am worried that adding Control Points will incorrectly label the region as white matter. I am attaching some pictures of slices where this is apparent. Thank you so much for your help! Best, Mariana

3 10

Error with TRACULA using dcm and nii
by Ferrier, Christopher Q. 01 Sep '17

01 Sep '17

Hello. We are trying to use TRACULA to analyze the structural connectivity of PD patients scanned on a 3 tesla Philips Ingenia. We have run the tutorial data without any problems but encounter errors when using our own data. We ran recon-all on all of our subjects without any problem and follow the exact steps that worked for the tutorial data but encounter different errors when using the dcm or nii version of the DTI scans. Our nii files go from scanner to CD to Osirix to DICOM to dcm2nii which gives us the nii files and the bvals and bvecs. Here is the error for the nii DTI scans (included bvals and gradients in the config file for the nii files). [Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial ERROR: flag -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial unrecognized -prep -c/Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial [Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c /Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial INFO: SUBJECTS_DIR is /Volumes/CFERRIER/Freesurfer_temp/PD800/diffusion_recons INFO: Diffusion root is /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT Actual FREESURFER_HOME /Applications/Freesurfer trac-preproc -c /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/dmrirc.local -log /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.log -cmd /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.cmd #------------------------------------- /Applications/Freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Aug 31 14:45:46 CDT 2017 mri_convert --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI_combined.nii... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999339, -0.0363145, -0.00163044) j_ras = (-0.0363101, 0.99508, 0.0921851) k_ras = (0.00172524, -0.0921834, 0.995741) writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz... cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvecs/PD800_bvecs.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvals/PD800_bvals.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals orientLAS /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz INFO: input image orientation is LAS INFO: input image determinant is -9.1875 mri_convert -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 -ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 7.38609 19.7949 1.17333 -rt nearest /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz mri_convert.bin -oni 128 -onj 128 -onk 50 -oid -0.999339 -0.0363145 -0.00163044 -ojd -0.0363101 0.99508 0.0921851 -okd 0.00172524 -0.0921834 0.995741 -oc 7.38609 19.7949 1.17333 -rt nearest /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz normalizing out_i_direction: (-0.999339, -0.0363145, -0.00163044) -> (-0.999339, -0.0363145, -0.00163044) normalizing out_j_direction: (-0.0363101, 0.99508, 0.0921851) -> (-0.0363101, 0.99508, 0.0921851) normalizing out_k_direction: (0.00172524, -0.0921834, 0.995741) -> (0.00172524, -0.0921834, 0.995741) $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999339, -0.0363145, -0.00163044) j_ras = (-0.0363101, 0.99508, 0.0921851) k_ras = (0.00172524, -0.0921834, 0.995741) Reslicing using nearest writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz... INFO: found /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals, copying INFO: found /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs, converting to LAS mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.bvecs /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.bvals /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals eddy_correct /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz 0 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0000 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0001 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0002 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0003 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0004 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0005 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0006 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0007 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0008 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0009 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0010 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0011 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0012 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0013 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0014 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0015 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0016 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0017 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0018 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0019 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0020 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0021 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0022 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0023 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0024 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0025 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0026 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0027 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0028 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0029 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0030 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0031 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0032 processing /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_tmp0033 mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.norot xfmrot /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.ecclog /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.norot /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs R: Subscript out of range. R: Subscript out of range. R: Subscript out of range. ln -sf /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/data.nii.gz mri_convert --frame 34 /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/lowb.nii.gz mri_convert.bin --frame 34 /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/lowb.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi.nii.gz... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999339, -0.0363145, -0.00163044) j_ras = (-0.0363101, 0.99508, 0.0921851) k_ras = (0.00172524, -0.0921834, 0.995741) keeping frame 34 ERROR: valid frame numbers are between 0 and 33 Darwin Christinas-iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Thu Aug 31 14:54:59 CDT 2017 Here is the error I encounter when running the original dicom files through tracula [Christinas-iMac:Freesurfer_temp/PD800/diffusion_recons] christina% trac-all -prep -c /Volumes/CFERRIER/Freesurfer_temp/PD800/dmrirc.tutorial INFO: SUBJECTS_DIR is /Volumes/CFERRIER/Freesurfer_temp/PD800/diffusion_recons INFO: Diffusion root is /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT Actual FREESURFER_HOME /Applications/Freesurfer trac-preproc -c /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/dmrirc.local -log /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.log -cmd /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/scripts/trac-all.cmd #------------------------------------- /Applications/Freesurfer/bin/trac-preproc #------------------------------------- #@# Image corrections Thu Aug 31 15:31:12 CDT 2017 mri_convert --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz mri_convert.bin --bvec-voxel /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm... Starting DICOMRead2() dcmfile = /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm dcmdir = /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm break DICOMRead.c:5228 Ref Series No = 601 Found 5 files, checking for dicoms WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm break DICOMRead.c:5228 WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm break DICOMRead.c:5228 WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm break DICOMRead.c:5228 Found 1 dicom files in series. WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips -- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm break DICOMRead.c:5228 WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD806_DTI.dcm break DICOMRead.c:5228 WARNING: tag image orientation not found in /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm ERROR: don't know how to get DWI parameters from --Philips Healthcare-- ERROR: GetDICOMInfo(): dcmGetDWIParams() 1 DICOM File: /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD809_DTI.dcm break DICOMRead.c:5228 First Sorting Computing Slice Direction WARNING: it appears that the image position for all slices is the same. This is a problem with the DICOM file. Using direction cosines from col and row to compute slice direction, but the output may be misoriented. Vs: 0 0 0 Vs: nan nan nan Second Sorting IsDWI = 0, IsPhilipsDWI = 0 Counting frames nframes = 1 nslices = 1 ndcmfiles = 1 PE Dir = UNKNOWN (dicom read) Loading pixel data TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0, -0, 0) j_ras = (-0, -0, 0) k_ras = (nan, nan, nan) writing to /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz... mri_probedicom --i /Volumes/CFERRIER/Freesurfer_temp/PD800/orig_nii/PD800_DTI.dcm > /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dcminfo.dat cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvecs/PD800_bvecs.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs cp /Volumes/CFERRIER/Freesurfer_temp/PD800/bvals/PD800_bvals.txt /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvecs.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvecs mv -f /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/bvals.tmp /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.bvals orientLAS /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig.nii.gz /Volumes/CFERRIER/Freesurfer_temp/PD800/TRAC_OUTPUT/PD800/dmri/dwi_orig_las.nii.gz mat = NULL! MatrixFree: NULL mat POINTER! mat = NULL! MatrixFree: NULL mat POINTER! mat = NULL! MatrixFree: NULL mat POINTER! INFO: input image orientation is III INFO: input image determinant is nan order: Subscript out of range. Darwin Christinas-iMac.local 14.5.0 Darwin Kernel Version 14.5.0: Thu Apr 21 20:40:54 PDT 2016; root:xnu-2782.50.3~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Thu Aug 31 15:32:20 CDT 2017 Thanks for your help. We tried to go through everything but nothing seems to be working.

1 0

QC cortical thickness measurements
by John Anderson 01 Sep '17

01 Sep '17

Dear FS experts, my apologizes if my question is a simple one. I am new to Freesurfer and I appreciate if you help me. After running recon-all on a T1 image I reached the final step and the analysis ran smoothly without any issues.. Now what I need to check in the output images to be sure that the cortical thickness measurements are correct and ready for cortical thickness group analysis like the one explained int this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis? If you can share any guide or a workflow sheet that can be followed to check the recons and the cortical thickness measurements systematically it will be highly appreciated! Thanks in advance for any help!! John

1 0

Open Letter to NIH Director Francis Collins
by Thomas Yeo 31 Aug '17

31 Aug '17

Dear Everyone, Please note the following NIH petition regarding the impending classification of basic science research as clinical trials: https://ipetitions.com/petition/open-letter-nih-collins Regards, Thomas

1 0

acceptable values for white matter on the T1.mgz volume
by Antonio 31 Aug '17

31 Aug '17

Dear FS community, I have a question regarding T1.mgz normalization values. Is there an established range of acceptable values for white matter around 110? For example, I'm getting values around 100 or so in some areas of low SNR (around the anterior temporal lobe region). Notwithstanding, the wm surfaces seem to look reasonable. I don't know if I should try control points to aid the normalization or if I should try tweaking the intensity correction parameters to somehow force these white matter voxels to be closer to 110. Thanks for your suggestions.

2 1

motion estimates
by James Welsh 31 Aug '17

31 Aug '17

Dear Freesurfer experts, I want to inquire if there are any tools in freesurfer that can help to evaluate T1 quality regarding motion and SNR. Thanks! James

2 4

aparc.stats files from FreeSurfer 6.0
by Mehta, Chintan 31 Aug '17

31 Aug '17

Dear FreeSurfer Users, I have run recon-all on data using both FreeSurfer versions 5.3.0 and 6.0. FS v6.0 generated files named lh.aparc.pial.stats and lh.aparc.stats, whereas FS v5.3.0 created only lh.aparc.stats. I wanted to verify two things: (a) Is it right that surface areas in lh.aparc.pial.stats correspond to pial surface (boundary between gray matter and CSF) of ROIs in the DK atlas, whereas lh.aparc.stats contains surface area at the boundary between gray matter and white matter at those ROIs? (b) There were differences between the values in the lh.aparc.stats from FS 5.3 and FS 6.0, despite my using the same data and same seed (i.e. -norandomness flag) for "recon -all" under both versions. Is it right that there are differences between the algorithms in FS 5.3 and FS 6.0 that could lead to this? Thank you. Best, Chintan

2 1

R: mris_anatomical_stats output
by stdp82＠virgilio.it 31 Aug '17

31 Aug '17

I have more that 50000 clusters (from over 100 subjects, 12 different conditions). Manual extraction is impossible!Any suggestions?ThanksStefano ----Messaggio originale---- Da: stdp82(a)virgilio.it Data: 19-ago-2017 2.38 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: [Freesurfer] mris_anatomical_stats output Hi list,how can I save the outputs of mris_anatomical_stats in xls file?Thanks Stefano

2 1

Software carpentry at the annual meeting of the Society for Neuroscience
by Ariel Rokem 30 Aug '17

30 Aug '17

Software Carpentry <http://software-carpentry.org/> is a non-profit volunteer organization whose members teach researchers computing skills. On November 9th-10th INCF <https://www.incf.org/> will hold a two-day Software Carpentry workshop at the George Washington University Marvin Center in Washington DC, to dovetail with the annual meeting of the Society for Neuroscience. The workshop will focus on software tools to make researchers more effective, allowing them to automate research tasks, track their research over time, and use programming to accelerate their research, and make it more reproducible. For details about the workshop please refer to the following web-page: https://incf.github.io/2017-11-09-sfn/ Participation is *free*, but because space is limited, we ask that participants apply to participate through the following web form: https://goo.gl/forms/09QyOPp3hFzw4ln63 *Application deadline is September 11th* Feel free to distribute this message widely among your colleagues, and to email me (Ariel Rokem: arokem(a)uw.edu) with any questions about the workshop. -- Apologies for cross-posting --

1 0

Call for Nominations - OHBM Student and Postdoc Special Interest Group {Disarmed}
by Michele Veldsman 29 Aug '17

29 Aug '17

*Call for Nominations - OHBM Student and Postdoc Special Interest Group * Dear OHBM Members, The OHBM Student and Postdoc Special Interest Group (SIG) are seeking nominations for our 2017-2018 committee. The SIG provides a community of shared interests for OHBM trainees. The committee aims to provide professional, personal and career development for OHBM trainees as well as social and mentoring opportunities at the annual meeting. Committee members benefit from being an integral part of the SIG, directing its activities, and working with the OHBM Executive and wider community. We are committed to diversity and equality and are seeking representation from trainees across the world. *Eligibility * - Nominees must be current students or postdocs. Students are defined as those working full time towards a graduate degree - M.S., Ph.D. or M.D. degree. Postdocs are individuals who are no more than four years after completing such a degree at the time of next annual meeting. - Nominees must be members of OHBM in good standing at the time of the next annual meeting - Nominees must be planning to attend the next two annual meetings in Seoul 2018 and Rome 2019 (and likely to attend the meeting in 2020). To nominate yourself for a position on the committee please fill out the nomination form and attach your CV: https://goo.gl/forms/iUF7wnMDhbdldGCG2 <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> Email ohbmtrainees(a)gmail.com <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> if you have any questions. *Nominations close on the 16th September 2017. * Kind regards, OHBM Student and Postdoc SIG *Organization for Human Brain Mapping (OHBM)* 5841 Cedar Lake Road, Suite 204 Minneapolis, MN 55416 USA Phone: 1 952-646-2029 | Fax: 1 952-545-6073 info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> www.humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> To opt out of OHBM emails, contact the OHBM Executive Office at info(a)humanbrainmapping.org <http://www.humanbrainmapping.org/i4a/etrack/track.cfm?rType=2&campaignID=35…> .

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