Freesurfer July 2018

freesurfer@nmr.mgh.harvard.edu

112 participants
165 discussions

PhD Studentship available at UCL
by Arman Eshaghi 23 Jul '18

23 Jul '18

External Email - Use Caution **Apologies for the wide distribution** Dear All, We have a PhD studentship for developing neuroimaging outcome measures in progressive multiple sclerosis clinical trials. The student will work with Prof Ciccarelli, Dr Chard and myself. https://www.findaphd.com/search/ProjectDetails.aspx?PJID=99251 I would be grateful if you could forward this email to potential candidates. Best wishes, ————————————————————————— Arman Eshaghi, MD, PhD Queen Square Multiple Sclerosis Centre 1st Floor, Russell Square House 10-12 Russell Square London WC1B 5EH Centre for Medical Image Computing (CMIC) Department of Computer Science University College London UK email: arman.eshaghi.14(a)ucl.ac.uk

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Re：segmentHA_T2.sh
by 墨初 23 Jul '18

23 Jul '18

External Email - Use Caution hello， I think RAM is enough。my computer is imac pro.There is 16G DDDR3. This process takes up about 1-2G. The total RAM occupied is 5G. Thanks Fiona Ding. ---------------- External Email - Use Caution Weird! Maybe you ran out of RAM memory? -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: <freesurfer-bounces at nmr.mgh.harvard.edu> on behalf of 墨初 <530337973 at qq.com> Reply-To: Freesurfer support list <freesurfer at nmr.mgh.harvard.edu> Date: Tuesday, 17 July 2018 at 13:40 To: freesurfer <freesurfer at nmr.mgh.harvard.edu> Subject: [Freesurfer] segmentHA_T2.sh External Email - Use Caution Dear freesurfer experts, when i run the command“segmentHA_T2.sh subject001 T2.nii T2 1” ,it runs as following: -------------- Making Left-Thalamus-Proper map to reduced label 10 -------------- Making Left-choroid-plexus map to reduced label 11 -------------- Making Left-VentralDC map to reduced label 12 -------------- Making Left-Accumbens-area map to reduced label 13 -------------- Making Unknown map to reduced label 14 Computing hyperparameters for estimation of Gaussians parameters znzreadInt: znzread failed No such file or directory Estimating typical intensities of molecular layer and alveus numberOfLabels: 2 Rasterizing mesh...here: 2 here2: 2 done Smoothing mesh collection with kernel size 1.500000 ...Smoothing class: 0 Smoothing class: 1 Smoothing class: 2 Smoothing class: 3 Smoothing class: 4 Smoothing class: 5 Smoothing class: 6 Smoothing class: 7 Smoothing class: 8 Smoothing class: 9 Smoothing class: 10 Smoothing class: 11 Smoothing class: 12 Smoothing class: 13 done numberOfImages = 2 Image: 0 Image: 2 Iteration 1 of 7 1 0.00035804 2 0.089592 fianally,it stop here and can't run anymore,no error reported。I didn't know what‘s wrong？ What can i do？ Thanks very much Fiona Ding

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The Problem Using "mris_ca_train"
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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Skull as an Object
by Zhang, Alexander D 22 Jul '18

22 Jul '18

Good Morning Freesurfer experts, I am trying to get the brain and skull as separate objects for use in blender. Is there any way to retain the skull in freesurfer? If not, would it be possible to retain all the mapping from the skullstrip feature? Best, - Alex

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periaqueductal gray
by Mr. Tass 22 Jul '18

22 Jul '18

External Email - Use Caution Hi, Just wondering if the periaqueductal gray is part of the automatic segmentation process and if we can obtain the volume. I checked the aseg table but didn't see it, however, I somehow remember seeing it before... Was it ever included? Thanks.

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Re: [Freesurfer] Skull as an Object
by Peled, Noam 21 Jul '18

21 Jul '18

Sure! You can find all about it in mmvt.org We also have a special panel for the skull: https://github.com/pelednoam/mmvt/wiki/Skull-panel Best, Noam ________________________________ From: Matti Hamalainen <msh(a)nmr.mgh.harvard.edu> Sent: Saturday, July 21, 2018 1:53:15 PM To: Bruce Fischl Cc: Freesurfer support list; Peled, Noam Subject: Re: [Freesurfer] Skull as an Object Hi Alex, Noam Peled (npeled(a)mgh.harvard.edu<mailto:npeled@mgh.harvard.edu>) can help you with this because he is using Blender in his MMVT. - Matti On Jul 21, 2018, at 1:45 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>> wrote: Hi Alex I'm not entirely sure what you mean. We do output boundary element models of the skull interfaces for MEG/EEG analysis if that is of interest. Matti Hamalainen can point you in the right direction for obtaining those models if you want cheers Bruce On Mon, 16 Jul 2018, Zhang, Alexander D wrote: Good Morning Freesurfer experts, I am trying to get the brain and skull as separate objects for use in blender. Is there any way to retain the skull in freesurfer? If not, would it be possible to retain all the mapping from the skullstrip feature? Best, - Alex ------------- Matti Hamalainen, Ph.D. Professor of Radiology, Harvard Medical School Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Building 149, 13th Street, Mailcode 149-2301 Charlestown, MA 02129-2060 USA e-mail msh(a)nmr.mgh.harvard.edu<mailto:msh@nmr.mgh.harvard.edu> Tel +1 617 726 0323 FAX +1 617 726 7422

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fcseedcor -- pca output for vcsf.dat and wm.dat
by Eryilmaz, H. Hamdi 20 Jul '18

20 Jul '18

Hi Doug and Freesurfers, I am using fcseedcor to compute the correlation between two time courses for each subject in my group. The command that I run is as follows: fcseedcor -s $subject -fsd resting -seed seed1.dat -seed seed2.dat -xreg global.waveform.dat 1 -xreg vcsf.dat 5 -xreg wm.dat 5 -xreg mcprextreg 6 -hpf .01 -lpf .08 -nskip 4 -o cor_s1s2.dat My first question is about the size of the vcsf.dat and wm.dat files. They seem to be (N+1)xN matrices, where N is the number of timepoints in the signal. Does this mean there are N+1 components for each time point (i.e., N+1 potential regressors to add)? What do they exactly correspond to and how do they relate to the average signal from the ventricles, CSF, and white matter? My other question is about the number of components to include for vcsf.dat and wm.dat. I have seen 5 recommended in examples, however, five components seem to explain very different amount of variance in different subjects and if I change this number for a given subject, I see substantial changes in the resulting correlation value. I would appreciate any suggestion on how to select an unbiased value for the number of components to include. Could including up to the component at which fixed percentage of cumulative variance is explained be a solution? Many thanks for your help! Best, Hamdi

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FreeSurfer License issue
by Carolina Bonivento 20 Jul '18

20 Jul '18

External Email - Use Caution Dear Sir/Madame, I recently subscribed the FS license (attached) but when I tried to run the 'recon-all’ (actually one of its steps, i.e. the MRI_ca_register) I received the following error message: ERROR: Invalid FreeSurfer license key found in license file /root/freesurfer/license.txt Following some instruction that I got previously, I replaced the .license with the license.txt in the $FREESURFER_HOME directory (in my case root/freesurfer) but I still get the same error message. Note that I’m running FreeSurfer through a Docker container running Ubuntu14 that is linked to the ‘freesurfer' folder on the' /User/home' of a macOS High Sierra (of course, Docker and the freesurfer folder are on the same machine). When I filled the license request form I’ve selected Linux/Intel as 'Operating System/Platform', as this is the OS of the Docker container. Is it possible that the issue is due to this? In that case, can I ask for a second license? Thank you in advance for your attention. Looking forward to hearing from you, I’m sending you my best regards, Carolina

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mri_binarize
by John Anderson 20 Jul '18

20 Jul '18

External Email - Use Caution Dear Freesurfer experts, I would like to inquire about the flag --subcort-gm in mri_binarize. It seems that the final product of this flag create a mask include the brain stem which is largely white matter. Why it was included in the subcortical gray matter structures? Thanks for any clarification, john

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Exporting results from QDEC
by Avi Gharehgazlou 20 Jul '18

20 Jul '18

External Email - Use Caution Hi experts, I want to make plots of my results that I have from QDEC, however, I'm having difficulty exporting values from QDEC. I examined LGI differences between groups, and I want to export my results, so the LGI values of significant between-group differences. Will you please tell me how I can do this? Thanks, Avi

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Freesurfer July 2018