Freesurfer July 2018

freesurfer@nmr.mgh.harvard.edu

112 participants
165 discussions

How to convert label to volume
by Dongsheng Wu 24 Jul '18

24 Jul '18

External Email - Use Caution Dear experts, Could you tell us how to convert label to volume? when I run this command "mri_label2vol --label lh.insular.label --temp /home/zwj/SCH_immune/A001 --identity --o insular.img", errors happened: corRead(): can't open file /home/zwj/SCH_immune/A001/COR-.info ERROR: reading /home/zwj/SCH_immune/A001 header In addtion, I am going to overlay a specific label to the template as following, could you tell me how to do it? Thanks Best Regards Wu

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recon-all cuda version 9.2 and 8.0
by charujing123 23 Jul '18

23 Jul '18

External Email - Use Caution Hi all How to download recon-all with GPU9.2 or 8.0? Thanks. Best 2018-07-24 charujing123

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Selecting vertices on label boundary for analysis
by Jacob Miller 23 Jul '18

23 Jul '18

External Email - Use Caution Hi Freesurfer team, In tksurfer, it's possible to display the outline of a label. Is there is a way to obtain the list of vertices that make up the outline of a label, so that I may select them from the label file? My goal is to perform an analysis that would only involve these boundary vertices (calculating the max distance between boundary vertices in a label, as a measure of label length). Thanks again! Jacob -- Jacob Miller Graduate Student, D'Esposito Lab Helen Wills Neuroscience Institute (HWNI) University of California, Berkeley https://despolab.berkeley.edu/

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symbolic link problem
by John Absher 23 Jul '18

23 Jul '18

External Email - Use Caution Hi, Running recon-all on sag T1 post-contrast MRI (for archival study) on virtualBox with centOS7 and freesurfer 6. The virtual box runs on a windows server and is allocated 8 processors and 16 GB memory by the windows server on which it resides. A citrix share provides the bulk of our filesystem storage space (/cifs). This filesystem appears not to allow symbolic links, such as these: rh.white.H rh.white.K lh.white.H lh.white.K These are symbolic links to [lr]h.white.preaparc.[HK], and recon-all stalls at the step during which these symbolic links are created. If we run the process in our /home directories on a linux filesystem, all is well, and recon-all runs correctly. However, only 8 GB of disc storage space there, and we have ~100 subjects to process. We thought we'd just run ~10 subjects or so, then move their data to the /cifs filesystem, but those 4 symbolic links won't copy. Questions: 1. If we ignore this error and copy everything else to the /cifs filesystem, is that OK, since the recon-all is complete? 2. If we try to run a GLM contrast on all the subjects (e.g., compare 50 to the other 50) in the /cifs filesystem, where we have space to keep all the data in one place, will the inability to create a symbolic link in that filesystem crash our analysis? 3. One post suggested copying the linked files into the SUBJECTS_DIR directory, but that won't work on /cifs and isn't necessary on the linux filesystem; is there another workaround? Thank you so much for you any guidance you can provide, and forgive me if there's some easy solution I've overlooked. John John R. Absher, MD, FAAN GHS Neurosciences jabsher(a)ghs.org<mailto:jabsher@ghs.org> 864-350-6655 (mobile)

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Fwd: The results of your email commands
by lucia quinones 23 Jul '18

23 Jul '18

External Email - Use Caution Dear experts, We are looking for a correlation between functional and structal ROIs on FSL and Freesurfer, but we have some questions about the atlas. 1. Are the Juelich Histological Atlas that can be downloaded with FSL the same as the cortical parcellation atlas that is used in Freesurfer? 2. How can we use a similar or equivalent atlas for ROI's correlation from both softwares? Thanks, Lucía

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adding additional manually-defined labels to atlas-derived .annot file
by James Hobart 23 Jul '18

23 Jul '18

External Email - Use Caution Hi Freesurfer community, I have an issue in adding a surface label to an annot file. I had a manually drawn .nii mask in native space for each subject which I have used mri_vol2surf to create a surface overlay and then mri_vol2label (with the surf argument) to create a surface label for the mask. I also have a custom parcellation of fsaverage which I have mapped to individual native space using mri_surf2surf. My issue is I want to combine the outputted binarymask.label file with the custom parcellation. My understanding is that I would need to combine the binarymask.label with the custom.parc.annot file. In order to do this wopuld I break down the annot file with mri_annot2label and then rebuild including the new binarymask.label? Could I also just add another row to the LUT from the custom.parc.annot file to allow this? And finally, how do I deal with the fact that the binarymask.label will overlap with other labels? Ideally I need to force the overwrite of vertex labels so that the binarymask.label is prioritised? BW James

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<no subject>
by 王子谦 23 Jul '18

23 Jul '18

External Email - Use Caution Hi, I am trying to do connectome to my patient with glioma. But now I’m stuck in parcellation the T1 image. Because the chaotic intensities of tumor totally mess up the outcome. Do you guys have any suggestion to the tumor? Is it any command about mask the tumor or any other method? Any suggestion would be thankful! Best Ziqian

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Hippocampal and amygdala subfields
by 郑凤莲 23 Jul '18

23 Jul '18

External Email - Use Caution Hi experts, I am using FS dev version for hippocampal and amygdala subfields. It's an automatic progress. Reviewers suggested that "Was the hippocampal and amygdala segmentation visually inspected?" We have visually inspected the segmentation and there is no error. I have an question about it. If there is uncorrected segmentation, how can I corrected it? Thanks very much. Look forward to you reply. Sincerely, Zheng

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(no subject)
by Maedeh Khalilian 23 Jul '18

23 Jul '18

External Email - Use Caution Dear FreeSurfer experts, I would like to use the FreeSurfer package to do a parcellation.Just for testing, I am using "buckner_data" and there is a step I have been stuck in.I have problem using "mris_ca_train" command.This is the whole code I run on my terminal to create my own atlas: [user@localhost ~]$ export FREESURFER_HOME=/usr/local/freesurfer [user@localhost ~]$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/subjects MNI_DIR /usr/local/freesurfer/mni [user@localhost ~]$ export TUTORIAL_DATA=/home/user/Desktop/ramezani/tutorial/ [user@localhost ~]$ export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs [user@localhost ~]$ cd $SUBJECTS_DIR [user@localhost tutorial_subjs]$ mris_ca_train -n2 rh rh.sphere.reg rh.aparc.annot good_output ./rh.my_atlas.gcs Usage: ------ mris_ca_train [options] <hemi> <canon surf> <annot file> <subject 1> <subject 2> ... <output file> [user@localhost tutorial_subjs]$ As you see it just goes to the next line and doesn't show any errors so I can get where the problem is from. That would be great if you could help me. Best regards;Maedeh

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nu_estimate_np_and_em and nu_correct error during recon-all
by Francis Houde 23 Jul '18

23 Jul '18

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to create a head model with T1w by creating tetrahedral head mesh with the simnibs program (documentation_2.0.1_preprocessing_scripts.pdf<http://www.simnibs.de/_media/docu2.0.1/documentation_2.0.1_preprocessing_sc…>). I want to simulate the effects of transcranial magnetic stimulations with the T1 of my subjects. When i run the mri2mesh command, which use some of the freesurfer commands, i get the following error with freesurfer : ncvarput: ncid 5: Protocol error miicv_put: MINC package entry point nu_estimate_np_and_em: crashed while running mincmath (termination status=768) nu_correct: crashed while running nu_estimate_np_and_em (termination status=768) ERROR: nu_correct Linux neurodebian 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt9-3~deb8u1 (2015-04-24) x86_64 GNU/Linux I've searched the list and no similar errors have been reported. Does anyone have any thoughts on how to trouble-shoot this one? Also, Ive attached the recon-all.log for two of my subjects in which i've encountered the error in case it's of any use. I've seen a couple of messages reporting this error in the mail archives but couldn't find any answer to correct this problem. Thank you in advance for your help ! Francis Houde Étudiant au doctorat en sciences des radiations et imagerie biomédicale Centre de recherche sur le vieillissement (Université de Sherbrooke) (819) 780-2220 # 45423 CIUSSS de l'Estrie CHUS 1036, rue Belvédère Sud - local 3441 Sherbrooke (Québec) J1H 4C4

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Freesurfer July 2018