Freesurfer March 2019

freesurfer@nmr.mgh.harvard.edu

114 participants
172 discussions

*.dcm to *.mgz
by Z Hessam 27 Mar '19

27 Mar '19

External Email - Use Caution Hello FreeSurfer Developers, I,m attempting to convert my dicom files to *.mgz, with command line in below: $ recon-all -i /data/14ZOGOO/1.dcm -autorecon1 -subjid d14zogoo but it exits with error and the recon-all.log file is attached. why this error occur and what should I do to solve it?

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mri_binarize --replace
by Song, Da-Yea 27 Mar '19

27 Mar '19

External Email - Use Caution Hello, I have a set of binary mask files that I'm trying to assign different values to. Currently I'm doing: mri_binarize --i sub001.nii.gz --o final_sub001.nii.gz --replace -117 2 mri_binarize --I sub002.nii.gz --o final_sub002.nii.gz --replace -128 2 The problem I'm having is that the values (V1) for each binary mask is not constant. For example, for one participant the values may be -117 whereas the values are -128 for another participant. Is there a way to set a range for the --replace option so that I can loop it through the subjects rather than having to do this command for each one separately? Any suggestions would be greatly appreciated! Thank you, Da-Yea ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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exact time of data acquisition per run
by Nasiriavanaki, Zahra 27 Mar '19

27 Mar '19

Dear Freesurfer experts Hi I am trying to extract the time of data acquisition for each run from the functional data and compare it with my paradigm files. I thought the numbers in DICOM file names (ie, MR.1.3.12.2.1107.5.2.43.67026.2019011316475911712728505 ) are correspondent with the date and time of data acquisition. But they don not exactly match with my paradigm files. Do these numbers represent the exact time of data collection for each run? Thanks Mona Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

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Trouble making ROI labels from .mgz file that has been converted from .nii.gz
by JD Knotts 27 Mar '19

27 Mar '19

External Email - Use Caution Hello FreeSurfer Developers, I am having difficulty trying to convert mrVista-defined ROIs in matlab into FreeSurfer label files. I'm starting with an atlas.mgz file (containing subject-specific visual ROIs based on the Kastner FreeSurfer atlas), and I should note that I can successfully make ROI .label files in FreeSurfer from this .mgz file using successive calls to mri_vol2surf and mri_cor2label. For reference, when I do this for the first Kastner ROI, the resulting label correctly has 1591 label voxels. However, part of my pipeline involves intersecting these ROIs with a localizer ROI that was defined in mrVista. To do this, I first convert the atlas.mgz file to .nii.gz using mri_convert as follows: mri_convert lh.atlas.mgz lh.atlas.nii.gz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1 After intersecting with the localizer in matlab, when I save a new .nii.gz file, convert back to .mgz, and run mri_vol2surf and mri_cor2label, I get the following error in mri_cor2label: ERROR: found no voxels matching id 1. To try to keep this short... as a sanity check I tried simply converting the lh.atlas.nii.gz file that pops out of the mri_convert step above directly back into .mgz (without modifying the .nii.gz file at all): mri_convert lh.atlas.nii.gz lh.atlas_reconverted.mgz --reslice_like subject_t1.nii.gz --resample_type nearest --out_data_type int --no_scale 1 When I run mri_vol2surf and mri_cor2label on the resulting lh.atlas_reconverted.mgz file, I don't get an error, but the resulting label file for the first Kastner ROI incorrectly finds 111 label voxels, none of which overlap with the correct 1591 label voxels above. So it appears that I'm making at least one mistake in the mri_convert step from nii.gz to .mgz above, but I'm struggling to figure out what it is. Any guidance on this would be greatly appreciated! Thank you for your time, JD Knotts 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 2) Platform: Mac OSX 10.11.6 3) Darwin Jeffreys-MacBook-Pro.local 15.6.0 Darwin Kernel Version 15.6.0: Thu Jun 23 18:25:34 PDT 2016; root:xnu-3248.60.10~1/RELEASE_X86_64 x86_64 4) recon-all.log: see attached for example subject

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Conversion of thalamic nuclei labels
by Valentina Mancini 27 Mar '19

27 Mar '19

External Email - Use Caution Dear all, I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got nice results with a good delineation of all the nuclei. Then, I wanted to use the label of the thalamic nuclei to select an ROI in the MGN and the MD to perform functional connectivity with cortical regions in SPM. Therefore, I converted the outputs of the segmentation (ThalamicNuclei.v10.T1.mgz and ThalamicNuclei.v10.FSvoxelSpace.mgz) into nifti files by using the command "mri_convert .mgz .nii". However, the resulting labels of the thalamus have a different resolution and I cannot visualize anymore the different thalamic subnuclei but only the entire thalamus. Do you have any suggestion to convert thalamic labels into nifti without losing the different subnuclei? Do you think that the thalamic segmentation is accurate enough to be used to perform functional connectivity? Thank you and best regards, Valentina Mancini

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Re: [Freesurfer] PetSurfer
by Shane Schofield 27 Mar '19

27 Mar '19

External Email - Use Caution Hi Doug, thanks for the explanation. My question is more related to how we might go about knowing what are the high binding regions for any tracer? If I am going to do an FDG-PET study, will the HB region parameters be different from a [11C]-PK11195 study for example? And secondly, might be these be different across subjects? Thanks for your help. Previous email :You should read up on the MRTM2. Basically, when you run MRTM1, it computes a separate k2 for each voxel eventhough the k2 should be the same across the entire brain (since it actually refers to the reference region). With MRTM2, you estimate the single k2 value from high binding regions.

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Thalamic nuclei segmentation
by 郑凤莲 27 Mar '19

27 Mar '19

External Email - Use Caution Hi experts, I have segmented the thalamic nuclei into 25 nuclei using the new FS version. However, when I input "freeview -v nu.mgz -v ThalamicNuclei.v10.T1.mgz:colormap=lut ", there is no 3D atlas in Freeview, just nu.mgz. What's the matter? Please help me. I am looking forward to your reply. Thanks very much. Sincerely, Zheng

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Re: [Freesurfer] Longitudinal Two Stage Model Question
by Arsenije Subotic 26 Mar '19

26 Mar '19

External Email - Use Caution Hi Doug, Thanks for getting back to me so quickly. Just to confirm, I can proceed to use the mri_glmfit analysis as shown on the group level tutorial? I'm not sure I can do the paired analysis since my subjects in one group are not matched with those from the other and one group has more participants than the other. I will however use the the link you gave me to compute the difference within one of my groups. Best, Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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Left and right pial surfaces crossing in medial cortex
by Matthieu VANHOUTTE 26 Mar '19

26 Mar '19

External Email - Use Caution Dear FS' experts, Using both T1 and FLAIR in recon-all to improve pial surfaces, I often have the case where pial surfaces from the left and right hemisphere are crossing in medial cortex (see attached images). Is it anormal and bad ? If so, How could I fix it ? Best, Matthieu

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Re: [Freesurfer] Longitudinal Two Stage Model Question
by Arsenije Subotic 26 Mar '19

26 Mar '19

External Email - Use Caution Sorry, I was actually able to compile a FSGD file that has a single line for each subject (containing the fsid base) along with gender and age at baseline. I ran this through the mris_preproc command (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) in order to stack the spc files which were previously cached. I guess my question really is can I now simply continue on and use the mri_glmfit instructions on the group analysis tutorial page or is there a special procedure because I am dealing with longitudinal data? I was planning on simply using contrasts i had designed before for my cross-sectional analysis, controlling for age at baseline and gender. Thanks and my apologies for all the questions! Arsenije --- Arsenije Subotic | MSc Student Department of Clinical Neurosciences Hotchkiss Brain Institute, University of Calgary | T2N 4N1, Canada Tel: (403) 918-6970 arsenije.subotic1(a)ucalgary.ca

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Freesurfer March 2019