Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30135 discussions

Question about mri_glmfit
by kinson li 28 Sep '16

28 Sep '16

*Hello,* *I would like to conduct an analysis using mri_glmfit but I'm getting this error:* *ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08* *I am appreciated you can help me solve this problem. * *My command was:* mri_glmfit --y age9vs8ml01.mgh --fsgd new.fsgd dods --C age9vs8mlmatrix.mtx --surf fsaverage lh --cortex --glmdir glmdir.age9vs8ml Design matrix ------------------ 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 1.000 0.000 8.000 0.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; 0.000 1.000 0.000 9.000; -------------------------------- ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Thanks Jincheng.

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Re Re Re Re: Question regarding mri_convert
by Tamara Tavares 28 Sep '16

28 Sep '16

The differences have been found in the outputs from the aseg file. Particularly, I am interested in the ventricles and the intracranial volumes. I have loaded both anatomicals in FreeView and toggled between them and have found no differences visually. I have attached the files (Via Google Drive since they are large). They are from the same participant. Thank you again, Tamara rawavg_MriConvert.mgz <https://drive.google.com/file/d/0B2XDrkcQhdARTFdYZHpwR2doTXc/view?usp=drive…> rawavgSlicer4.mgz <https://drive.google.com/file/d/0B2XDrkcQhdARV1dtZW1PZ1Z1ODA/view?usp=drive…>

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Anatomy File Orientation Question
by Sepeta, Leigh 28 Sep '16

28 Sep '16

Hi all, Sorry to re-post: 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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REPOST cluster feature extraction from qdec output
by Damien MARIE 28 Sep '16

28 Sep '16

Dear FreeSurfers, Sorry for the repost. I’m still trying to extract the residuals of cortical surface area from a qdec analysis with two factors (2 levels) and 2 covariates. I tried this command line: mri_segstats --in /home/damien/bin/freesurfer/subjects/qdec/RH_Dys-CT_CSA_AgeGenderWRCSA/y.mgh --sum toto --annot fsaverage rh mc-z.abs.th23.sig.ocn --avgwf RH_Dys-CT_CSA_AgeGenderWRCSA.dat I’ve got a text file with 9 columns (number of clusters) and 69 lines (number of subjects). Now I am not 100% sure it’s really the residuals (y.mgh) so I would be glad if somebody could tell me please. Best, Damien Original post: Dear experts, I would like to know what is the best and simplest way to extract cortical surface area and thickness from clusters obtained after a Monte Carlo correction. This is a group comparison I did with qdec including gender as discrete variable + age and mean thickness or whole hemispheric surface area as nuisance factors, so I would like to get the feature residuals after the removal of the covariate effects. I am sorry, I saw several posts about that but for me it’s not completely clear what command line I should use to get tables for this… Thank you and best, Damien Damien MARIE Post-doctoral Fellow damien.marie(a)unige.ch +41 22 379 08 49 ----------------------------------------------------------------------------------------- Brain and Language Lab Department of Clinical Neuroscience Biotech Campus 9 Chemin des Mines 1202 Genève http://www.brainandlanguagelab.org -----------------------------------------------------------------------------------------

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TRACULA results
by Kang, XJ 28 Sep '16

28 Sep '16

Hi, I downloaded FreeSurfer development version built on Sep 20. Then I ran the "trac-all" for the same set of DWI data four times. The volume and averaged DTI parameters of the fiber pathways, which found in the file ~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, are different for each run. The maximum differences can be upto +-90% for volume, +-10% for FA_avg. Any ideas for the inconsistency? Thanks. XJ Kang

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Re: [Freesurfer] Freesurfer Digest, Vol 151, Issue 30
by KALEY E ELLIS 28 Sep '16

28 Sep '16

Hi Ruopeng, When I try to open it, this is part of the error message that appears: freeview -v 2000_2/mri/T1.mgz 2000_2/mri/brainmask.mgz:colormap=heat:opacity=0.4 libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error: BadValue (integer parameter out of range for operation) 2 Extension: 150 (Uknown extension) Minor opcode: 3 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: GLXBadContext 160 Extension: 150 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x6000ba X Error: 0 0 Extension: 150 (Uknown extension) Minor opcode: 26 (Unknown request) Resource id: 0x0 X Error: BadMatch (invalid parameter attributes) 8 Extension: 150 (Uknown extension) Minor opcode: 11 (Unknown request) Resource id: 0x6000b8 If I run glxgears, this appears: [edwards@guero ~]$ glxgears libGL error: No matching fbConfigs or visuals found libGL error: failed to load driver: swrast X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 150 (GLX) Minor opcode of failed request: 3 (X_GLXCreateContext) Value in failed request: 0x0 Serial number of failed request: 28 Current serial number in output stream: 30 [edwards@guero ~]$ Thank you! Kaley Message: 6 Date: Fri, 23 Sep 2016 18:53:45 -0400 From: Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] freeview display problem To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <732E27D8-179E-4B66-8762-7BF26C1DFF81(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset="utf-8" Is there any error message on the terminal? What happens if you run ?glxgears? command? Does it run? Best, Ruopeng > On Sep 23, 2016, at 4:35 PM, KALEY E ELLIS <keedwards2(a)wisc.edu> wrote: > > Hello FreeSurfer Developers, > > I am attempting to open freeview to view the brainmask on a subject in our study. Everything looks normal, except there is no image displayed (see attachment). Could you please let me know how I can fix this? > > Thank you, > Kaley > > Associate Research Specialist > Center for Healthy Minds > Waisman Center for Brain Imaging and Behavior > University of Wisconsin-Madison > <Screen Shot 2016-09-23 at 3.34.25 PM.png>_______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>

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TR: volume to surface for ROI already in orig space
by Alain Imaging 28 Sep '16

28 Sep '16

________________________________ De : Alain Imaging <alain_imaging(a)outlook.com> Envoyé : lundi 26 septembre 2016 17:17 À : freesurfer(a)nmr.mgh.harvard.edu Objet : volume to surface for ROI already in orig space Hi everyone, I've used a couple of ROIs that have been drawn in the mni space for connectivity analysis. Since I have my connectivity results shown on a surface, I want to show the ROIs in the same way. I have checked with freeview, and the ROIs are correctly placed in the fsaverage/orig.mgz space. I wanted to use mri_vol2surf in order to reach my aim, however this command require a transformation matrix, and in this particular case I don' really know which one to use, as I don't want to change space. I thought that maybe i could provide an identity matrix, but I don't know what would it be an acceptable format for it. Have you got any suggestion ? Alain

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Do you suggest to denoise T1 before feed it to Freesurfer
by Zhengchen Cai 27 Sep '16

27 Sep '16

Hi Freesurfers, In order to get the better segmentation and surfaces by Freesurfer, do you think it is necessary to denoise T1 before feed it to Freesurfer? Since there are several advanced MRI denoising methods which are not covered in FS preprocessing, I though it would be better to perform one of them before FS. However, one of my concern is that those denoising will modify the intensity of the image and this may effect or even conflict with the processing in FS such as intensity normalization or registration to the template. Based on my experiences of FSL, most of time, the denoising methods will make the segmentation worse. For FS, I've tried just few subjects and the segmentations were better than feeding the raw MRIs. What is your suggestion in general case? or maybe it is not reasonable at all to denoise before FS? Many thanks. Best regars, Zhengchen

2 1

Freeview Loading Volumes
by Robert Kraft 27 Sep '16

27 Sep '16

I use Freeview on a daily basis as my primary image viewer. I like it a lot and found it to be tremendously useful. I am usually interested in opening images in the current directory where I launched Freeview from the command line. I know you can load multiple images at once from the command line but occasionally I want to load an additional image. Ideally, I would like Freeview when I want to load a volume to open up the file explorer tool in the current directory. Instead, it opens up in another directory and I have to click down several directories before finding the file that I want. Freeview has been consistently opening up in the same directory. I just can’t figure out why it picks that directory. If someone could tell me if it is possible for Freeview to open the file browser in the directory it was launched I would be extremely grateful. Thanks for your help in advance, Bob

2 1

Coordinates of particular volumes
by Aziz Nanthaamornphong 27 Sep '16

27 Sep '16

Dear Freesurfer experts, How can we get the coordinates (X, Y, Z) of a particular volume? I couldn't find any functions or command to do that. Thank you in advance. Aziz.

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