Freesurfer September 2016

freesurfer@nmr.mgh.harvard.edu

133 participants
200 discussions

Freeview error: Surface does not contain valid volume geometry information
by Claudia Dacquino 20 Sep '16

20 Sep '16

Hi all, after doing GLM analysis I'm trying to run freeview to see results, but I get this warning: Surface does not contain valid volume geometry information. It may not align with volumes and other surfaces. What's wrong? I'm using 5.1 version. Thanks to all. Claudia -- Dott.ssa Claudia Dacquino, Specialista in Neuropsicologia Laboratorio di Neuropsichiatria Dipartimento di Neurologia Clinica e Comportamentale IRCCS Fondazione Santa Lucia via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 51501575 web: http://www.neuropsichiatrialab.com <http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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local intensity inhomogeneity
by Jason Tourville 20 Sep '16

20 Sep '16

Hello freesurfers, We've seen some poor surface reconstructions due to local inhomogeneities that remain in the brainmask volume. We see omission of significant portions of brain tissue due to signal fall off (both gray and white voxels are darker than in surrounding area) that we are unable to current through control points or other manual interventions. Can anyone suggest a tool for correcting latent local inhomogeneities? Is anyone aware of a manual tool that allows one to "brighten" the voxels from some point outward at some falloff rate? Any help would be greatly appreciated. Best, Jason

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LGI and MATLAB
by Alan Francis 20 Sep '16

20 Sep '16

Hi Marie - I have MATLAB and the Image processing toolbox on my MAC. Unfortunately, I am unable to get FreeSurfer to recognize this (see below) , so I am getting an error. Is there any way to overcome this? Thanks, Alan afrancis-mac:~ afrancis$ export FREESURFER_HOME=/Applications/freesurfer afrancis-mac:~ afrancis$ source /Applications/freesurfer/SetUpFreeSurfer.sh -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl afrancis-mac:~ afrancis$ export MATLABPATH=/Applications/MATLAB_R2015a.app/bin afrancis-mac:~ afrancis$ export PATH=${MATLABPATH}/bin:${PATH} afrancis-mac:~ afrancis$ recon-all -s DM55 -localGI INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-rw- 1 root wheel 948660 Sep 16 09:50 /Applications/freesurfer/subjects/DM55/scripts/recon-all.log Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64 INFO: current FREESURFER_HOME does not match that of previous processing. Current: /Applications/freesurfer Previous: /cm/shared/freesurfer /Applications/freesurfer/subjects/DM55/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Sep 16 09:55:23 EDT 2016 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin afrancis-mac.mclean.harvard.edu 14.5.0 Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64 x86_64 recon-all -s DM55 exited with ERRORS at Fri Sep 16 09:55:23 EDT 2016 For more details, see the log file /Applications/freesurfer/subjects/DM55/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf(a)bwh.harvard.edu <ezra_wegbreit(a)brown.edu> afrancis(a)mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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Re: [Freesurfer] White matter surface don't change after editing
by Cong 20 Sep '16

20 Sep '16

> On Sep 10, 2016, at 1:15 AM, 3110103623(a)zju.edu.cn wrote: > > Hi Dear Bruce > Thanks very much for your reply, I improved min_border_white to 100, the lh.white line shrinks but still is far out in some area, and I notice many topological defect appears as a result. > I failed to upload subject through ftp, it's always appear an error called "553 Could not create file", so I send a subject to you through FileDrop. Can you receive a file named Cong2Bruce.zip? > Thanks again for your help. > > Best Wishes > Cong Chen > > Date: Thu, 8 Sep 2016 10:12:29 -0400 (EDT) > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > Hi Cong > > you could try using expert options to modify the mris_make_surfaces > parameters. It looks like you white surface is too far out. Try > increasing min_border_white and/or increasing max_gray. If you can't get it > working feel free to upload the entire subject dir and we will take a look > > cheers > Bruce > > > On Thu, 8 Sep 2016, Cong wrote: > > Hi dear all > I attach a new picture to illustrate this problem. I erased some voxels in wm.mgz and rerun. The lh.orig(blue line) looks well, but lh.white(yellow line) don?t along the white surface in some area. Could anyone give me some advice? Thanks very much. > > Best wishes > Cong Chen > > > Date: Sun, 4 Sep 2016 15:15:42 +0800 > From: Cong <3110103623(a)zju.edu.cn <mailto:3110103623@zju.edu.cn>> > Subject: [Freesurfer] White matter surface don't change after editing > > Dear freesurfer team? > I have some MRI images from a GE scanner, it seems that images? quality is poor because grey matter is bright in so much area and these grey matter is included in wm.mgz. So I deleted wrong voxels in wm.mgz by freeview and rerun through command ? recon-all -autorecon2-wm -autorecon3 -subjid subjname?. But ?h.white (yellow line) don?t change after rerunning as you can see in the attached picture. Is this problem caused by deleting too many voxels and how to fix it? Thanks very much. > > Regards > Cong Chen

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Re: [Freesurfer] Dev builds not found
by Leila Reddy 20 Sep '16

20 Sep '16

Hi Bruce,Thanks for your reply. Does anyone on the list have access to the tar file of the latest dev build that they could put on some other site or in a public Dropbox folder? I totally changed my system and don't have a working version of Freesurfer/FS-FAST anymore and am pretty much stuck. Otherwise, do you think I should try to install an older version of perl? Sorry to cause you trouble,Thanks, Leila

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Display FSL PALM(permutation) stats in freeview
by Ajay Kurani 20 Sep '16

20 Sep '16

Hello Freesurfer Experts, I was running permutation simulations on cortical thickness data and I had an issue with non-orthogonal covariates with mri_glmfit-sim -perm. I then tried FSL's PALM which is an extension of randomize to calculate threshold free stats. I saved the output as logp(which is similar to qdec I believe), however I have not been able to load the stats files correctly. The output of palm is lh.thickness_tfce.mgz for my various contrasts. 1) Is .mgz the proper format for the stats files or do I need to convert this to another type like .mgh etc? 2) Can I display this in freeview or is another program needed? I also tried tksurfer but when I loaded the stats file as an overlay nothing displayed. I want to make sure that the stats is loaded as an overlay in freeview/tksurfer and if so, do I need to select anything special so that it scales the logp values correctly? Thanks, Ajay

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mris_calc cluster infos
by Nick Corriveau Lecavalier 19 Sep '16

19 Sep '16

Hi Freesurfer team, I have a 2 Group (MCI, CTL) x 2 (Time1, Time2) protocol. As suggested in an earlier discussion, I measured the rate atrophy for each group between my two time points. Then I applied the clusterwise correction for multiple comparison, which give a lot of information about each group (for example, number of clusters, # of voxels, regions where there's a significant difference). Then I used mris_calc to compute the difference between my groups. My question is: Is there a way to obtain the same informations on the group difference? Since mris_calc doesn't have a .log as output, I can't compute mris_glmfit-sim on it and I cannot get any infos on the cluster summary. Regards, Nick Corriveau-Lecavalier, B.Sc. (Hons.) Étudiant au Ph.D. recherche/intervention, option neuropsychologie clinique Coordonateur à la recherche, Association étudiante des cycles supérieurs en psychologie de l'Université de Montréal (AÉCSPUM) Université de Montréal Centre de recherche de l'Institut universitaire de gériatrie de Montréal, bureau M7819

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Anatomy File Orientation Question
by Sepeta, Leigh 19 Sep '16

19 Sep '16

Hi all, I am trying to bring my FreeSurfer brainmask into SPM and then to coregister it (along with some ROIs from FreeSurfer) to the same subject's mprage already processed (coregistered to functional data) in SPM. To do this, I used: mri_convert brainmask.mgz brainmask.nii.gz (then used gunzip) and then looked at the brainmask and mprage in SPM and they both seem to be oriented correctly (left is left, right is right for each one--using anatomical landmarks as the guide). However, in reading up on this topic, many people advise using commands like these (often with RAS) when converting mgz to nii: mri_convert --in_type mgz --out_type nii --out_orientation RAS brainmask.mgz brainmask.nii.gz OR mri_convert --out_orientation RAS -rt nearest --reslice_like <reference.nii or reference.nii.gz> <input.mgz> <output.nii> OR mri_convert -rl rawavg.mgz -rt nearest brainmask.mgz brainmask.nii.gz Are any of the options (-rl, RAS, etc) in the last 3 commands listed necessary when going between mgz/nii for freesurfer to spm analyses if you know that the mgz and nii files are in the same orientation? Thank you, Leigh <mailto:lsepeta@childrensnational.org> ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

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FoV in additional scan
by Vaz pandolfo, Renata 19 Sep '16

19 Sep '16

Dear Eugenio, We have another question about the Hippo Sf Segmentation with an additional scan. Some of our additional scans (FLAIRs or T2s) have a bigger field of view as compared to the T1 (ex.: they cover more of the neck almost up to the shoulders of the subjects, while the T1 has the "normal" FoV). Should the additional scan be cropped or preprocessed in any way (ex.: bias field correction)? And if so, should we process the T1 in the same way or is it generally recommended to just use the raw images? Thank you! Renata

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FLAIR for hippo subfield segmentation with an additional scan
by Vaz pandolfo, Renata 19 Sep '16

19 Sep '16

Dear FS experts, I have a question about the "segmentation with an additional scan - multispectral segmentation" on the hippocampal sf segmentation, FS dev. 6.0. For controls on which I had already run recon-all -all, I added the T2 sequence with the following command: recon-all -s <subject_name> \ -hippocampal-subfields-T1T2 <file name of additional scan> <analysisID> Now, if I want to do the same thing with FLAIR as the additional input, which flag should I use? Thank you, Renata

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Freesurfer September 2016