Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30064 discussions

Philips and Toshiba dicom tag Read - error
by M Janani 06 Sep '17

06 Sep '17

Hi Team, We would like to process the MRI data obtained using Philips and Toshiba scanners. Can we do it using Freesurfer? Thought the reconstruction process got completed successfully, we got DICOM read error while fetching DWI parameters in the beginning of the reconstruction process. Can I neglect that error? Attached log for reference. Regards, Janani ::DISCLAIMER:: ---------------------------------------------------------------------------------------------------------------------------------------------------- The contents of this e-mail and any attachment(s) are confidential and intended for the named recipient(s) only. E-mail transmission is not guaranteed to be secure or error-free as information could be intercepted, corrupted, lost, destroyed, arrive late or incomplete, or may contain viruses in transmission. The e mail and its contents (with or without referred errors) shall therefore not attach any liability on the originator or HCL or its affiliates. Views or opinions, if any, presented in this email are solely those of the author and may not necessarily reflect the views or opinions of HCL or its affiliates. Any form of reproduction, dissemination, copying, disclosure, modification, distribution and / or publication of this message without the prior written consent of authorized representative of HCL is strictly prohibited. If you have received this email in error please delete it and notify the sender immediately. Before opening any email and/or attachments, please check them for viruses and other defects. ----------------------------------------------------------------------------------------------------------------------------------------------------

2 1

rh.white and rh.pial surface manual edit
by Farhad Ghaseminejad 06 Sep '17

06 Sep '17

Hello FreeSurfer experts, I was wondering if you have any suggestions on how to fix the error in the rh.white and rh.pial surface in the Orbitofrontal cortex as shown in the screenshots attached. https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sha… <https://drive.google.com/drive/folders/0B64fNVlVdTBYOVhJMXJyTjZVSTQ?usp=sha…> Best, Farhad

2 1

Talairach registration error
by Ariana Vajdi 05 Sep '17

05 Sep '17

Hello, Hope this message finds you well. I was beginning to run recon-all on a dataset and was encountering a problem with the talairach registration. I've encountered this error before here and there, but I've been receiving the same error for every scan that I've been trying to run, and I'm not sure why. It's also the first time I've used NIFTI files as the input - not sure if that's a contributing factor. I've also tried the -use-mritotal flag without any luck. These are the errors I receive: WARNING: neither NIfTI-1 qform or sform are valid WARNING: your volume will probably be incorrectly oriented ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050) Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. I would appreciate your help. Thank you! Warmly, Ariana

2 1

Ventricle Volumes Decreasing over time?
by Tamara Tavares 05 Sep '17

05 Sep '17

Hello, I used the default longitudinal stream to calculate ventricular volumes over time. When I examined the difference score (longitudinal-baseline) I noticed that for some participants ventricular volumes *decreased*. The same site, scanner and scanning protocol was used for both baseline and longitudinal scans. I processed the cross, template and longitudinal time points on the same computer using the same Freesurfer version (v 5.1). Furthermore, this decrease in ventricular volume is evident before and after manual corrects were made to the aseg file. Is it common to see an *decrease *in ventricular volume over time? Can this be due to Freesurfer variability or slight differences in the scanner over the two time points? Thank you in advance for your help. Best, Tamara

2 1

controlling for Sex in a model using two continuous variables onto CTh
by Uquillas, Federico D'Oleire 05 Sep '17

05 Sep '17

Dear FreeSurfer experts, We have run a vertex-wise analysis regressing a continuous variable onto cortical thickness on the surface, and would like to verify that our contrast that uses Age and Sex as covariates was defined correctly, especially since there is probably more than one way to control for a binary variable like Sex. On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it suggests to make two regressors, one for Males, and one for Females, where for the former a 1 is indicative of the Male category, and a 1 on the latter is indicative of the Female category. However, using that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the error: matrix is ill-condition or badly scaled, condno=2.01889e+07. We believe this may be due to the fact that Male and Female categories are autocorrelated and Freesurfer likes variables to be de-meaned. Running a FSGD file with only Age and our variable of interest via a DOSS contrast of [0 1 0] works without any errors. We thus created an FSGD file where we have Sex as our third variable (in addition to our continuous variable of interest and one demeaned continuous covariate), coding 1s for Males and 0s for Females, and we used a DOSS contrast of [0 1 0 0]. This provided us with a map that makes sense with our expectations. We would like to verify if this is doing what we believe it is doing; that is, looking at the relationship of our continuous variable or interest after accounting for age and sex. Any thoughts would be greatly appreciated. Thank you so much. Best, Fred

4 8

Error with TRACULA using dcm and nii
by Ferrier, Christopher Q. 05 Sep '17

05 Sep '17

Hi Freesurfer Team!. 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

sub-cortical analysis
by John Anderson 05 Sep '17

05 Sep '17

Hi Dr Greve, I am using pet surfer to analyze suv images. I followed all the steps in wiki, I used the option mgx then I fed the images mgx.{ctxgm,subctxgm,gm} into surface based analysis for left and right hemispheres. I want to inquire about the sub cortical analysis. 1. I assume the analysis for sub cortical gray matter (i.e. using the images subctxgm) is volumetric. Is this correct? 2. Are the following steps correct for sub cortical gray matter analysis mri_vol2vol --mov subctxgm.nii.gz --reg reg.dat --tal --talres 2 --talxfm talairach.xfm --nearest --no-save-reg --o subctxgm.tal2mm.nii.gz mri_mask subctxgm.tal2mm.nii.gz $FREESURFER_HOME/subjects/fsaverage/mri.2mm/subcort.mask.mgz subctxgm.tal2mm_subc.nii.gz & Concatenate all subjects together using mri_concat smooth using mri_fwhm (what is the recommended smoothing for suv)? Then Group analysis: mri_glmfit --y all.suvr.tal2mm.subc.sm10.nii --fsgd fsgd.dat --C contrast.mtx --glmdir dir mri_glmfit-sim --glmdir dir --grf 1.3 pos --cwpvalthresh 0.0166 for "mri_glmfit-sim" in subcortical structure is the flag grf correct or cache? Thanks in advance! John

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R: Re: Map of covariance
by stdp82＠virgilio.it 05 Sep '17

05 Sep '17

Hi, e.g., by considering two or more groups, I would like to map the clusters reporting the covariance between the functional connectivity or cortical thickness (dependent variable) and age, tacking in account the group differences. Instead, I'm not interested to map the group differences, taking in account the nuisance factors. Thanks, Stefano >----Messaggio originale---- >Da: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >Data: 5-set-2017 18.12 >A: <freesurfer(a)nmr.mgh.harvard.edu> >Ogg: Re: [Freesurfer] Map of covariance > >I don't understand what you are asking. can you elaborate? > > >On 08/30/2017 12:50 PM, stdp82(a)virgilio.it wrote: >> Hi list, >> by applying a design e.g. 4GV1 in fsgd I could assess the dependence >> of group differences taking in account the effect of covariate. >> Anyway, where I should look if I want assess the the map showing the >> clusters in which the dependent variable is associated to covariate, >> tacking in account the group difference? Please could you suggest my >> the path? >> Thanks >> >> Stefano >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >-- >Douglas N. Greve, Ph.D. >MGH-NMR Center >greve(a)nmr.mgh.harvard.edu >Phone Number: 617-724-2358 >Fax: 617-726-7422 > >Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >www.nmr.mgh.harvard.edu/facility/filedrop/index.html >Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >The information in this e-mail is intended only for the person to whom it is >addressed. If you believe this e-mail was sent to you in error and the e-mail >contains patient information, please contact the Partners Compliance HelpLine at >http://www.partners.org/complianceline . If the e-mail was sent to you in error >but does not contain patient information, please contact the sender and properly >dispose of the e-mail. > >

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MNI average brain in Freesurfer space
by Anna Kasdan 05 Sep '17

05 Sep '17

Hi everyone, Is there a freesurfer file/file format for the *average* MNI brain (as opposed to fsaverage which is just based on different subjects)? Or is there a way to turn MNI coordinates into freesurfer space? Thanks so much! Anna Research Assistant, NYU

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Re: [Freesurfer] Reliability of labeling procedure in the same scan
by Phoolan Devi 05 Sep '17

05 Sep '17

I mean the hippocampal volume in the aseg... so, it's not normal? Bruce Fischl <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…> Sat, 26 Aug 2017 11:24:44 -0700 <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date…> do you mean the hippocampal volume in the aseg or in the subfields? On Sat, 26 Aug 2017, anonymous anonymous wrote: Hi all, Without noticing I run recon-all twice on the same scan of the same subject and we noticed there are some differences, at least in the hippocampal volume estimation. Is it normal? If it is, why is it so? Thank you so much for your help This is a great community! _______________________________________________ Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine athttp://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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