Freesurfer

freesurfer@nmr.mgh.harvard.edu

21 participants
30071 discussions

Freeview command line option for multiple screenshots
by peng 01 Mar '17

01 Mar '17

Dear all, I have several different overlays on the same brain surface. When I want to run freeview in command line and take screenshots automatically, I need to restart freeview and load the surface for each screenshot. Is it possible to keep the program on and only change overlays and take screenshots for each of them? It seems possible in GUI but I don't know how to realise in command line. Another question is, when I have the overlay on, before taking the screenshot, is it possible to mark a location, by e.g. a dot/circle/square/cross/etc, the colour of the marker shall be independent of the overlay. I have the index of this location in the surface vertices. Thank you in advance. best Peng

2 1

Longitudinal hippocampal subfield registered to base
by Worker, Amanda 01 Mar '17

01 Mar '17

Hi All, I have applied the hippocampal subfield segmentation algorithm to each of my time points that have been longitudinally processed. I am now trying to register these back into base space using: mri_convert -T BASE/mri/transforms/TP_to_base.lta -rl BASE/mri/norm.mgz -rt nearest --out_type mgz TP.long/mri/lh.hippoSfLabels-T1.v10.mgz TP.long/lh.hipp.base.mgz Firstly, when I try to overlay lh.hipp.base.mgz for each timepoint onto BASE/mri/T1.mgz they do not align. Do you have any idea why this is? Secondly, the output seems to be for the whole hippocampus, is there a way to do this for each subfield individually? Any advice would be much appreciated, Amanda

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(no subject)
by Manuel Delgado 01 Mar '17

01 Mar '17

Dear all, I am carefully starting up with the basics for analysis of 3T mri images. After having done the recon all I am about to begin the review and editting process where needed. However, I am now a bit overwhelmed. Is there any logical or recommended order to proceed with the several potential editting steps? Is it possible to edit all the parts (i.e. skull striping, wm, pial surface, etc) and performe an only final recon with all the needed flags? Best, Manuel

1 0

multiple expert options files/ wm and control points
by miracle ozzoude 28 Feb '17

28 Feb '17

Hello Freesurfer, I have couple questions. 1) If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30) and I want recon-all to execute both commands. Should I create 2 different expert opts files or 1 expert opts file with both commands in it? Also, how do I include the expert flag with recon? 2) If I have added control points and wm edits to a subject, it is accurate to start from control points? i.e., recon-all -autorecon2-cp -autorecon3 3) Lastly, I am playing around with mri_fill command and I did like to know what -T flag does? Thank you Best, Paul

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Freeview default cursor
by Rockers, Elijah D. 28 Feb '17

28 Feb '17

Hello, I could not find any information on changing the cursor via command line. My goal is to persistently change the default cursor style/color, I was going to create an alias on my system. Thanks, Eli Houston Methodist. Leading Medicine. U.S. News & World Report has recognized Houston Methodist as one of the nation’s top 20 hospitals, placing it for the second time on the magazine’s prestigious Honor Roll. It is also designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

2 1

mri_convert error: 'GetDICOMInfo(): dcmGetDWIParams() 7' in FS6.0
by Gustav Mårtensson 28 Feb '17

28 Feb '17

Hi, I have a problem when executing the following command on images scanned on 1.5T Philips (Intera) in FS 6.0: recon-all -i 0e242a36-5390-4358-9f92-eb9f62c48124/ADNI_032_S_0187_MR____________MPRAGE__br_raw_20060213164320687_1_S11617_I11073.dcm -subjid 4450a7a0-27e9-42bc-99ab-1c15519ad9a4 -all -mprage -qcache -hippocampal-subfields-T1 -brainstem-structures -cw256 which during mri_convert produces the error: ERROR: GetDICOMInfo(): dcmGetDWIParams() 7 DICOMs from other scanners works fine as far as we know. When processing them through 5.3.0 we didn't get any errors like this, regardless of scanner If we just copy the mri_convert binary file from FS 5.3.0 to FS 6.0 the errors disappears. Would this be the recommend approach to solve our issues? We are running on Ubuntu 16.04 LTS with FS version freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. I've included recon-all.log case it is of interest. Thank you for your help! -- Gustav Mårtensson | PhD student Division of Clinical Geriatrics Department of Neurobiology, Care Sciences and Society Karolinska Institutet

2 1

ocn.nii & ocn.annot mismatch
by Tuominen, Lauri Johannes 28 Feb '17

28 Feb '17

Hi all, Has anyone encountered a mismatch between the ocn.nii & ocn.annot files. I'm doing a fsfast group analysis with freesurfer5.3 and the ocn.nii file is missing one region that comes up in all the other files as well as in the annot. A fix for this would be much appreciated. Please see the attachement Cheers! Lauri Tuominen

2 1

How to output particular area from stats subdir
by Jing Gu 28 Feb '17

28 Feb '17

Dear FreeSurfer Developers, By using the following code, we can get volume data of different areas from stats file. asegstats2table --subjects N01 --meas volume --tablefile aseg_stats.txt How can I get information of one or two areas, such as hippocampal? thanks Best, Gina

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chose between 5.3 and 6.0
by ? ? 28 Feb '17

28 Feb '17

dear FS community: now i have more than 200 subjects which already finished recon-all with 5.3, since 6.0 released, i wonder should i re-run them with 6.0 as lots of changes like different surf-map and registration. i ran a bit of them as test and i found the pial problems were more than 5.3, and it seems some subcortical structures were vanished in the brainmask.mgz, though the aseg.mgz looked good. i wanna ask is my problem serious or it is usual with 6.0, and which version you think is better for cortical volume and surface thickness reserch? best regards weiwei west china hospital ________________________________ weiqi77777(a)live.com

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Re: [Freesurfer] editing topological defect
by Antonin Skoch 28 Feb '17

28 Feb '17

Dear Shane, the "topological defect" in FreeSurfer jargon means that the estimated surface contains errors like "holes" or "handles". See PPT from FreeSurfer course http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt or https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData XL (=extra large?) defect often means large error in previous steps of recon-all, usually skullstrip or white matte segmentation. In some cases the error is automatically corrected, but not always. To see, what is happening, I would suggest to inspect brainmask.mgz or wm.mgz and correct errors. You can also find more information on the forum, there are quite large amount of posts related to topological defects. For example: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg30763.html Antonin Skoch Hi Freesurfer Team, I am running recon-all on Freesurfer version 6. A few of my subjects have “XL defect detected …” and their recon-all have been running for more than 20 hours. I hope this is not a silly question, but will this XL defect be corrected eventually…? Another question, what are “defects”? Is there anything I could do to the raw T1 before recon-all? Thanks! Shane

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