Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

SPM to FreeSurfer
by Rachel Wagner 19 Jun '22

19 Jun '22

External Email - Use Caution Hello, I am trying to take my SPM images and cortically project them with free surfer (SpmPainting - Free Surfer Wiki (harvard.edu)<https://secure-web.cisco.com/1o3IHzvB09pwh3UU64pSKXFgTUAafyWmRKJ9lNBgTQW81z…>. As it might be quite obvious, I have very little experience using these softwares. I am typing in the suggested code as follows: developer@developer-VirtualBox:~$ mri_convert $SUBJECTS_DIR/subjectname/mri/brain.mgz brain.img mri_convert /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz brain.img reading from /usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz... error: mghRead(/usr/local/freesurfer/7.2.0/subjects/subjectname/mri/brain.mgz, -1): could not open file developer@developer-VirtualBox:~$ ^C developer@developer-VirtualBox:~$ Is there something I am doing incorrectly? Thank you! Rachel

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Freeview GUI overlay and registration
by Kuo, Yi-Ling 19 Jun '22

19 Jun '22

Hi Freesurfer experts, I am trying to use the Freeview GUI to load fMRI BOLD activation data (analyzed in FSL) and project on the inflated surface. I used the feature “Overlay/Load generic” and was prompted to select overlay file and/or apply registration. The selected overlay file didn’t seem to project on the right spot on the inflated surface as would be seen in T1. If registration was the issue, what registration file should be selected in the Freeview GUI? My Freeview was updated. Thank you very much for helping. Irene

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-hires flag sometimes breaks recon-all
by Schneider, Christoph 19 Jun '22

19 Jun '22

Hi, I have 7T MP2RAGE data of 25 individuals with an isotropic 0.7mm voxel resolution. I initially ran FS with the -hires flag to preserve the additional detail, but in 4 cases this crashed the process, while running the same image without the -hires flag works fine (surfaces visually inspected). I just wanted to know what could be the cause for this difference in behavior between the two options. Many thanks in advance, Chris Christoph Schneider, PhD Postdoctoral Research Fellow Harvard Medical School Massachusetts General Hospital Gordon Center for Medical Imaging

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mri_label2vol misaligned for subcortical atlas
by Christopher Pirrung 19 Jun '22

19 Jun '22

External Email - Use Caution Hi Freesurfer Devs, I’m attempting to transform the Harvard-Oxford subcortical atlas (obtained from https://secure-web.cisco.com/1Tup0RI4qms0go1SEsu5ke-k7Cz5iL5tezC3TmgzZcvjKq…) to my subjects’ native anatomical space to create individualized versions of this atlas. To do so I used the line: mri_label2vol --seg H-O_subcortical_parcellation_thr50.nii --temp rawavg.mgz --o HO-subcort.mgz --regheader H-O_subcortical_parcellation_thr50.nii based on the recommendation from https://secure-web.cisco.com/1bcvHE7fWzSmfgBGxlww4NvvAmOJRlTofNlaCk_OCSbG9A… However, when I load the rawavg.mgz and individualized atlas in freeview, the atlas is ~30 mm away from being aligned. Do you have any idea why this might be the case or recommendations to get a better alignment? Thanks! Chris

2 1

Incorporating samseg segmentation into the recon-all pipeline
by Julian McGinnis 19 Jun '22

19 Jun '22

External Email - Use Caution /Hello everyone,/ /We have been utilizing freesurfer for our brain morphometry and processing pipelines, and have recently tested the samseg segmentation algorithm on a clinical cohort./ /With respect to some regions, we currently prefer its results to the ones generated by the standard freesurfer segmentation algorithm. / /As SAMSEG only provides volume calculation (please correct me if I am wrong) and does not feature cortical thickness measurements,/ /I was wondering if the recon-all pipeline can be modified to utilize the samseg segmentation instead, and if so, which script(s) or chain of commands would be a good starting point to implement this./ /Looking forward to your feedback,/ /Julian / Julian McGinnis PhD Candidate TUM-Neuroimaging Center, School of Medicine, Technical University of Munich, Munich, Germany Department of Computer Science, Technical University of Munich, Munich, Germany Email:julian.mcginnis@tum.de

2 1

(no subject)
by Bouchra Guelib 18 Jun '22

18 Jun '22

External Email - Use Caution Hi, I try to do something like that, Would anyone help me -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: Guelibbouchra(a)gmail.com

1 0

Setting Location?
by Rachel Wagner 17 Jun '22

17 Jun '22

External Email - Use Caution Hello, I am attempting to convert an image file and am getting the following error: developer@developer-VirtualBox:~$ mri_convert Combined_roi_meanRD.nii Combined_roi_meanRD.img mri_convert Combined_roi_meanRD.nii Combined_roi_meanRD.img reading from Combined_roi_meanRD.nii... error: niiRead(): error opening file /home/developer/Combined_roi_meanRD.nii I believe this is due to the location I have stored it (desktop); how do I set the location? Thank you, Rachel Wagner

1 0

TRACULA Configuration Question
by Daliah Ross 17 Jun '22

17 Jun '22

External Email - Use Caution Hi FreeSurfer experts, I am planning to use TRACULA and have a question regarding the configuration file and whether we can start with already processed data. We have already run some steps involved in the TRACULA configuration script, which take several hours per subject to complete. Specifically, we already ran topup to handle B0 distortions and already processed eddy distortion corrections. Could this be bypassed when configuring TRACULA so we are not redoing these hours, or does it have to be run within TRACULA? Thank you, Daliah -- *Daliah Ross, M.A.* | dross3(a)mail.yu.edu Ph.D. Candidate, Clinical Psychology with Health Emphasis Neuropsychology Concentration Ferkauf Graduate School of Psychology, Yeshiva University Albert Einstein College of Medicine *pronouns: she/her/hers*

1 0

about the error on running TRACULA using tutorial data
by Xin Qi 17 Jun '22

17 Jun '22

External Email - Use Caution Hi I downloaded the FreeSurfer tutorial data ( https://secure-web.cisco.com/1tDso4rjIlURcoFeNGyGUBBs1I7uczKauIIt12c78g81fR…) and tried to test TRACULAR. In the preprocessing step by running $trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial, I got the following error messages. ERROR: length of pathway list (lh.cst_AS rh.cst_AS lh.ilf_AS rh.ilf_AS lh.unc_AS rh.unc_AS fmajor_PP fminor_PP lh.atr_PP rh.atr_PP lh.cab_PP rh.cab_PP lh.ccg_PP rh.ccg_PP lh.slfp_PP rh.slfp_PP lh.slft_PP rh.slft_PP) and endpoint label ID list ERROR: () do not match There may be something wrong with the demo dmrirc.tutorial configuration file, which is attached to the email. Please help me with how to fix the problem. Thank you very much. Best regards Xin

2 3

I cannot start my first subject.
by refaat el-said 17 Jun '22

17 Jun '22

External Email - Use Caution Good morningI installed Oracle VM virtual box i am able to work on the tutorial patient bert but when I copied dicom file of a patient I could not work with it.Are there instructions on how to import dicom files to the virtual box machine and the first step to prepare them for analysis?Refaat

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