Freesurfer November 2020

freesurfer@nmr.mgh.harvard.edu

107 participants
149 discussions

mri_vol2surf
by Alberto Del Cerro Leon 19 Nov '20

19 Nov '20

External Email - Use Caution Hello, I have a couple of questions: 1. I asked before how to obtain AAL labels on Freesurfer. I am following your instructions, but I don't know how to load the AAL onto my T1w template to ensure everything aligns 2. Secondly, I tried to run mri_vol2surf with the following command: mri_vol2surf --src /home/neuroimage/fsl/FreeSurfer/AAL.nii --regheader MNI --projfrac 0.5 --hemi lh --out /home/neuroimage/fsl/FreeSurfer/AAL-lh.img. However I obtained an error "ANALYZE FORMAT ERROR: ncols 161783 in volume exceeds 32768". How can I fix it?

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dcmunpack command not found
by Cláudia Sofia de Matos Alves 19 Nov '20

19 Nov '20

External Email - Use Caution Hello, i have been trying to use the dcmunpack command and it always says command not found, i searched in the archives and some said it could be because the tcsh or csh wasnt installed however i have both installed (which tcsh and which csh return their location) and when i run dcmunpack it always returns "command not found", how can i solve this? Thank you!

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question about PVC of PETSurfer
by 蒋袁芳 19 Nov '20

19 Nov '20

External Email - Use Caution Hello Freesurfer, We know that the freesurfer7 has given a new module to separate hippocampal subfields in MRI image, but we encoumter problems in registering the PET image with MRI image. We find that the resolution radio of PET image is not enough, it made the SUVr of hippocampal subfield we get is not accurate. So we want to use the PVC function of PETSurfer. Whether the PETsurfer output the result of PET image after PVC ? so that we can use it directly to registering with MRI image. If it doesn't output the result, can we save it in some ways? Thank you for your guidance.

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Single Hemisphere Option Availability for Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal)
by Park, James 18 Nov '20

18 Nov '20

External Email - Use Caution Dear Freesurfer team, Thank you so much for your support for this software thus far. As we were considering using the module for segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal), we came across an interesting scenario: Due to certain conditions for some subjects we seek to analyze, we would like to only run this module of freesurfer on one hemisphere. I understand that recon -all has this option (-hemi ?h) but found that there was no documentation regarding single hemisphere segmentation of the Hippocampus / Amygdala. Could you let us know if there are any hidden options that enable single hemisphere processing or workflows that allow for this? Thank you so much for your help as always. Sincerely, James Park ________________________________ This e-mail message (including any attachments) is for the sole use of the intended recipient(s) and may contain confidential and privileged information. If the reader of this message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this message (including any attachments) is strictly prohibited. If you have received this message in error, please contact the sender by reply e-mail message and destroy all copies of the original message (including attachments).

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recon-all for 0.85 isotropic images error
by Lee Subin Kristine 18 Nov '20

18 Nov '20

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to run recon-all (v.6) on T1- and T2-weighted images that have 0.85mm^3 isotropic voxels I have entered the command as below, with the T2, T2pial, cm, cw256 flags. recon-all -i $T1_DIR/"oT1_"$subj.nii -T2 $T2_DIR/"oT2_"$subj.nii -T2pial -cm -cw256 -subject $subj"_test" -all However, I keep getting the error as follows. ERROR! FOV=272.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. I'm guessing that conforming to the small voxel size results in a FOV that is out of limit? However, when I check the orig.mgz file it looks fine. (It has an image dimension of 320 x 320 x 320). Even when I include the flag -cw256 as the error message says, I still get the same error message. (Also, I cannot find any documentation about the -cw256flag on the help page). I have pasted the full log below. Thank you for your help. Best regards, Kristine ------------------------------------------------------------- subin@ubuntu:/mnt/hgfs/subindata/MYELIN-QSM/SCRIPT$ ./run_fs_1 INFO: all volumes are conformed to the min voxel size Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c INFO: SUBJECTS_DIR is /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW Actual FREESURFER_HOME /usr/local/freesurfer Linux ubuntu 4.15.0-112-generic #113~16.04.1-Ubuntu SMP Fri Jul 10 04:37:08 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/usr/local/freesurfer/bin/recon-all' -> '/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/scripts/recon-all.local-copy' -cw256 option is now persistent (remove with -clean-cw256) /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test mri_convert /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz mri_convert.bin /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99998, -0.00515189, -0.00357438) j_ras = (0.00515192, 0.999987, 0) k_ras = (0.00357433, -1.83865e-05, 0.999994) writing to /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz... #-------------------------------------------- #@# T2/FLAIR Input Fri Oct 30 05:19:16 PDT 2020 /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test mri_convert --no_scale 1 /mnt/hgfs/subindata/MYELIN-QSM/BRL_T2/oT2_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/T2raw.mgz mri_convert.bin --no_scale 1 /mnt/hgfs/subindata/MYELIN-QSM/BRL_T2/oT2_BRL_0004.nii /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/T2raw.mgz $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/hgfs/subindata/MYELIN-QSM/BRL_T2/oT2_BRL_0004.nii... TR=3200.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99998, -0.00515189, -0.00357438) j_ras = (0.00515192, 0.999987, 0) k_ras = (0.00357433, -1.83865e-05, 0.999994) writing to /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/T2raw.mgz... #-------------------------------------------- #@# MotionCor Fri Oct 30 05:19:23 PDT 2020 Found 1 runs /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz Checking for (invalid) multi-frame inputs... WARNING: only one run found. This is OK, but motion correction cannot be performed on one run, so I'll copy the run to rawavg and continue. cp /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test mri_convert /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig.mgz --conform_min mri_convert.bin /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig.mgz --conform_min $Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $ reading from /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/rawavg.mgz... TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0.99998, -0.00515189, -0.00357438) j_ras = (0.00515192, 0.999987, 0) k_ras = (0.00357433, -1.83865e-05, 0.999994) changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig.mgz... **************************************** ERROR! FOV=272.000 > 256 Include the flag -cw256 with recon-all! Inspect orig.mgz to ensure the head is fully visible. **************************************** Linux ubuntu 4.15.0-112-generic #113~16.04.1-Ubuntu SMP Fri Jul 10 04:37:08 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux recon-all -s BRL_0004_test exited with ERRORS at Fri Oct 30 05:19:38 PDT 2020 For more details, see the log file /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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Striatum Mask for Choi et al 2012
by RENXI LI 18 Nov '20

18 Nov '20

External Email - Use Caution Hi Freesurfer Experts: In $FREESURFER_HOME/average/Choi_JNeurophysiol12_MNI152 directory, there are a striatum parcellation masks based on functional connectivities to the cortical networks by Yeo et al 2011. I would like to register this striatum parcellation mask to each subject’s striatum mask. But to create the striatum mask in the native subject space using mri_binarize, which segmentation file do you recommend to use and which segmentations should I be including in the mask to cover all regions in Choi’s striatum mask? Best, Renxi

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T1 and DTI nifti data stored after running recon-all and trac-all
by Zeng, Qi 17 Nov '20

17 Nov '20

External Email - Use Caution Hi, I run both recon-all and trac-all for each subject. Where are the original T1 and DTI data stored in the output files? Thank you so much! Best, Qi

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problem about PVC of PETSurfer {Disarmed}
by qianqiansci 17 Nov '20

17 Nov '20

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distance between two vertices in Freeview
by Nasiriavanaki, Zahra 17 Nov '20

17 Nov '20

Dear Freesurfer experts Hi I was trying to measure the dimensions of a surface ROI in a flatten map on Freeview. I used the 3D scale bar to measure the longest diameter of the ROI. My question is how the scale bar is calculating the distance between the two points? Is it the euclidean distance between the two vertices? I calculated the euclidean distance in matlab between the two vertices (using their x and y coordinates) , and the number I get, is much higher than what I see in freeview. I wonder why this discrepancy is happening? I appreciate if you could please let me know the answer to my question. Thanks MOna Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Postdoctoral Fellowship in Cognitive Neuroscience - Braga Lab @ Northwestern University {Disarmed}
by Ania Holubecki 17 Nov '20

17 Nov '20

External Email - Use Caution We are seeking a postdoctoral fellow to join the Braga Lab ( https://secure-web.cisco.com/1HqJOdOxFbbEvFFuelHbM7FlG-fov0-xk1W0oKrv-pXwn-…) in the Department of Neurology at the Northwestern University Feinberg School of Medicine. Under the mentorship of Rodrigo M. Braga, PhD, the lab uses and develops neuroimaging techniques to characterize brain network organization and function at the level of individuals. Research topics include the nature of brain regional specialization for language, recollection and mental imagery, as well as the mechanisms of cross-network interaction at high spatiotemporal resolution. Fellows will assist with ongoing research studies using methodologies including functional magnetic resonance imaging (fMRI), intracranial electroencephalography (iEEG) and brain stimulation. Fellows will have opportunities to participate and lead in data collection and analysis, mentorship of students and staff, presentations at national meetings, and writing publications. Requirements: Applicants must have a PhD (or equivalent doctoral degree) in neuroscience or a related field, from an accredited institution. Fellows must receive their degree by the start of training or have received their degree no more than five years ago. Candidates must be a U.S. citizen or be eligible to work in the United States (after obtaining an appropriate visa). Desired skills: Strong candidates will have prior experience with programming and neuroimaging (broadly defined), including data collection and analysis, as well as conducting behavioral experiments. Interested candidates should email a cover letter briefly describing their research interests and qualifications, a curriculum vitae, as well as the names and contact information for three references to Anna Holubecki at: anna.holubecki(a)northwestern.edu Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes, including veterans and individuals with disabilities. Women, racial and ethnic minorities, individuals with disabilities, and veterans are encouraged to apply. Hiring is contingent upon eligibility to work in the United States.

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Freesurfer November 2020