Freesurfer

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30084 discussions

PET image format
by Marina Fernández 29 Nov '20

29 Nov '20

External Email - Use Caution Dear experts! I am using PetSurfer and I have a PET dataset that is in ecat format (.v). I would like to convert the images to nifti format to start processing the data. What function can I use to convert the images? How can I check that the left-right orientation doesn't flip? Thank you in advance! Marina.

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eddy_correct with DTI {Disarmed}
by Wei Shao 29 Nov '20

29 Nov '20

External Email - Use Caution Hi, Freesurfer team, My name is Weishao, Here is a problem that bothers me a lot I try to run DTI. I have loaded the FSL module and use the most recent version of Freesurfer. it's appreciated if someone can help. Thanks. Here is the script. dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s /home/weishao/scratch/rawdata/sub-AVP6176/ --o /home/weishao/scratch/rawdata/sub-AVP6176/ Here is feedback -rw-r----- 1 weishao weishao 49041968 Sep 9 11:41 /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz INFO: SUBJECTS_DIR is /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects dt_recon logfile Tue Oct 27 16:19:28 EDT 2020 VERSION dt_recon 7.1.0 setenv SUBJECTS_DIR /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/subjects cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi /project/6019291/shared/software/2017/Core/freesurfer/7.1.0/bin/dt_recon --b sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bval sub-AVP6176_ses-01_dir-sfs_run-01_dwi.bvec --i sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz --s /home/weishao/scratch/rawdata/sub-AVP6176/ --o /home/weishao/scratch/rawdata/sub-AVP6176/ gra95 weishao /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct ECRefTP 0 #@#------------------------------- Converting input Tue Oct 27 16:19:28 EDT 2020 cd /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi mri_convert /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz mri_convert /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz reading from /scratch/weishao/rawdata/sub-AVP6176/Ses-01/dwi/sub-AVP6176_ses-01_dir-sfs_run-01_dwi.nii.gz... TR=4000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-0.999608, 0.017447, -0.021891) j_ras = (0.0104682, 0.958258, 0.285714) k_ras = (-0.0259621, -0.285373, 0.958065) writing to /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz... #@#------------------------------- Eddy/Motion Correct Tue Oct 27 16:19:44 EDT 2020 cd /scratch/weishao/rawdata/sub-AVP6176/ectmp eddy_correct /scratch/weishao/rawdata/sub-AVP6176/dwi.nii.gz /scratch/weishao/rawdata/sub-AVP6176/dwi-ec.nii.gz 0 /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/eddy_correct: line 95: /cvmfs/ soft.computecanada.ca/easybuild/software/2017/avx2/Compiler/intel2016.4/fsl/5.0.11/fsl/bin/imglob : *No such file or directory* Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value *ERROR: when running eddy_correct* Best, Wei

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mris_pmake error - freadFloat: fread failed
by Nasr, Shahin,Ph.D. 29 Nov '20

29 Nov '20

Hi Surfers, For one subject, when I run mris_pmake as below: mris_pmake --subject <Subject_Name> --hemi lh --surface smoothwm --mpmProg pathFind --mpmArgs vertexStart:<Start Vertex>,vertexEnd:<End Vertex> --mpmOverlay euclidean I get the following error: mris_pmake error - freadFloat: fread failed This error appears irrespective of the Start/End vertex, as far as I see. I guess this error is because a file in the subject's brain recon is corrupted. But unfortunately, the error message is not helpful. I even tried to open the error.log. But I do not see any further info there. Any suggestions? Shahin

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RHEL 7 and tkmedit {Disarmed}
by Tracy Riggins 29 Nov '20

29 Nov '20

External Email - Use Caution Dear Freesurfer Gurus We just upgraded our server to RHEL 7. However, we want to do some white/pial edits on some brains using Freesurfer 5.1.0. We know this is an old version, but we are combining some new data with a lot of old data that had been processed before in 5.1.0 and ... we want to use the old version. However, when using tkmedit the error below was received. Can you help? Thanks in advance, Tracy =================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer(a)nmr.mgh.harvard.edu : : Now exiting... *Contents of the the file .xdebug_tkmedit here:* tkmedit started: Wed Nov 18 10:50:06 2020 /cell_root/software/freesurfer/5.1.0/sys/tktools/tkmedit.bin SLP003_practice_KK brainmask.mgz -aux wm.mgz -surfs $Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /export/data/seahorse_ncdl/SLP/data/white_pial_practice Set subject home dir to /export/data/seahorse_ncdl/SLP/data/white_pial_practice//SLP003_practice_KK Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x27f57890, isSource=/export/data/seahorse_ncdl/SLP/data/white_pial_practice//SLP003_practice_KK/mri/brainmask.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=brainmask.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=6, argv=/cell_root/software/freesurfer/5.1.0/sys/tktools/tkmedit.bin ) 02: Loading volume brainmask.mgz 01: main() 01: Parsing command line arguments 00: 00: ] -- Tracy Riggins, Ph.D. Associate Professor Secretary, Cognitive Development Society Department of Psychology 4094 Campus Drive Biology/Psychology Building Room 2147J University of Maryland College Park, MD 20742 (301) 405-5905 http://secure-web.cisco.com/1BXBdC5OSLi3H7WL6XT9HhLP6upr-VMDdJcVP0_Zi60l0rJ… https://secure-web.cisco.com/1707dQrUylXr-ioQLaAeJuIXFc8V8l-3l8Gsf5fqQmfGql… riggins(a)umd.edu Pronouns: she/her/hers

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calculating hemisphere total grey matter volume
by Vicente Ferrer 29 Nov '20

29 Nov '20

External Email - Use Caution Hello Freesurfer, Once I had run reconall, I tried to calculating left hemisphere total grey matter volume and right hemisphere total grey matter volume by doing the sum of: TGM_left=lhcortexvol + Left-Cerebellum-Cortex + (Left-Thalamus-Proper + Left-Caudate + Left-Putamen + Left-Pallidum + Left-Hippocampus +Left-Amygdala +Left-Accumbens-area +Left-VentralDC) using the volumes values of the aseg.stats file. I did it like this because of the definitions of TGM in this webpage: https://secure-web.cisco.com/18pk-Ax0hgeQLjPCil_KNGcr0ZuCL3RBLq8NqkvLiWHU5V… However I did a saninty check and compared the TGM_estimated=TGM_left + TGM_right. with the measurement in the aseg file: Measure TotalGray, TotalGrayVol, Total gray matter volume. They are similar but not the same. Which makes me wonder if this is not the proper ay of calculating it. Therefore: which is the best way of calculating left hemisphere total grey matter volume and right hemisphere total grey matter volume in a separated manner? Thanks in advance, Vicente Ferrer Predoctoral Researcher BCBL http://secure-web.cisco.com/1Y80FAmAIDLnW-nPDCMBRDUQbmyy9_KQJaimWnm60B6mbmp… Legal disclaimer/Aviso legal/Lege-oharra: http://secure-web.cisco.com/1HBxObiSRumyzSCM72mU7-knka-loKiKejfXjeLERlyDL2E…

2 1

qdec replacement
by Pagliaccio, David (NYSPI) 29 Nov '20

29 Nov '20

External Email - Use Caution Hello I was just wondering if there were any updates on a FSv7 replacement for QDEC for vertex-wise cortical thickness analyses? Or if there were any recommendations for analyses in other programs? Thanks! David -- David Pagliaccio, Ph.D. Assistant Professor of Clinical Neurobiology (in Psychiatry) Columbia University Irving Medical Center Assistant Research Scientist Division of Child and Adolescent Psychiatry New York State Psychiatric Institute 1051 Riverside Drive New York, NY 10032 phone: 646-774-5556 Email: david.pagliaccio(a)nyspi.columbia.edu<mailto:david.pagliaccio@nyspi.columbia.edu> Pronouns: he/him

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smoothing on ?h.w-g.pct.mgh files
by Enrico Collantoni 29 Nov '20

29 Nov '20

External Email - Use Caution Dear Freesurfer experts, I computed the gray to white matter signal intensity ratio using the pctsurfcon command and extracted the ?h.w-g.pct.mgh files. How can I conduct a smoothing procedure on these surface files? Thanks for your help, -- Enrico Collantoni MD, Ph.D., Psychiatrist University of Padua Neuroscience Department

2 1

use different parameters of MRI DICOM
by 王颖喆 29 Nov '20

29 Nov '20

External Email - Use Caution Hello Freesurfer Developers, I'm attempting to analyze data using freesurfer. The dataset we used includes two different series of MRI DICOM: The first series (n=562) was collected using the following paremeters: t1_fl3d (Voxel Size = 0.9×0.9×1.5mm, FOV = 220 mm, TR = 21ms, TE = 7.65ms, Flip Angle = 30⁰); The second series (n=300) : MPRAGE(Voxel Size = 1×1×1mm, FOV = 256mm, TR = 2300ms, TE = 2.98ms, Flip Angle = 9⁰). All brain MRIs were performed on the same 3.0T Siemens scanner. I'd like to know if it is accpetable to include both of these imagings in one analysis? Is there any pre-processing step need to be done? Thank you! Yingzhe Wang

2 1

error message {Disarmed}
by Ambulatorio SNA FEDERICO II 28 Nov '20

28 Nov '20

External Email - Use Caution Dear Freesurfer team, I'm running a group analysis where I'd like to compare myelination between two groups regressing out cortical thickness, age and sex. My FSGD file is: GroupDescriptorFile 1 Title Func Class HC Class CMT Variables Age gender Input fs_VF HC 46 Female Input fs_RF HC 24 Female ....... My group.diff.mtx is: 1 -1 0 0 0 0 0 My command line: mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness_age_gender.glmdir *But unfortunately I get this wrong message: * RROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit.bin --y rh.t1t2ratio_30_fmed_3sm_decurv.fsavg.mgh --fsgd age_gender.fsgd --pvr rh.thickness_30.fsavg.mgh --C group.diff.mtx --surf fsaverage rh --cortex --glmdir rh_allbrain_t1t2_group_thickness_age_gender.glmdir 2. The FSGD file (if using one) 3. And the design matrix above Attempting to diagnose further SumSq: Min=0.000000 (col 5), Max=146.140350 (col 3) The scale is much different between columns 5 and 3, you may want to normalize by subtracting the mean and dividing by the standard deviation. Column 5, all values are 0 Column 6, all values are 0 Columns 5 and 6 are the same Can you please help me? Thank you very much Raf <https://secure-web.cisco.com/1wUz9v9uYsJZHEMIX9ov8a61ikcAm6idKqX4eyutNBtobO…> Mail priva di virus. http://secure-web.cisco.com/1u95FL6P0fuXqFu5_WySmigs4cTD1aGD0opSNlDIfm7U18E… <https://secure-web.cisco.com/1wUz9v9uYsJZHEMIX9ov8a61ikcAm6idKqX4eyutNBtobO…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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recon-all 7.1.1
by James Hartzell 27 Nov '20

27 Nov '20

External Email - Use Caution Hi Andrew Thanks for the suggestions. I removed freesurfer and reinstalled just 7.1.1. When I try to run the original patch you suggested I still get permissions problems, even with sudo. (base) jameshartzell@Jamess-MacBook-Pro ~ % which freesurfer /Applications/freesurfer/7.1.1/bin/freesurfer (base) jameshartzell@Jamess-MacBook-Pro freesurfer % cd $FREESURFER_HOME/bin (base) jameshartzell@Jamess-MacBook-Pro bin % sudo mv recon-all recon-all.backup Password: (base) jameshartzell@Jamess-MacBook-Pro bin % sudo curl https://raw.githubusercontent.com/freesurfer/freesurfer/fs-7.1/scripts/reco… > recon-all zsh: permission denied: recon-all Here's hoping you can send another fix! Cheers James -- James Hartzell, PhD (2x) Donostia-San Sebatián, Spain Center for Mind/Brain Sciences (CIMeC), The University of Trento, Italy Center for Buddhist Studies, Columbia University, USA

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