Freesurfer August 2017

freesurfer@nmr.mgh.harvard.edu

145 participants
233 discussions

Generating Surfaces from Labels
by Zach Humphrey 11 Aug '17

11 Aug '17

Hello All, I have been attempting to convert Label files generated using mri_annotation2label into surface files for use in external programs. In order to do this I first need to convert the label files into freesurfer binary. I have attempted to use the mri_label2vol function to generate an mgz file which could then be converted into freesurfer binary but this has resulted in mgz files which depict a solid cube rather than any brain structure. Any ideas as to why this could be? I would also prefer to avoid ever converting the label files to a volume as converting the volume file to a surface file results in a lower quality than if the file has been maintained as a surface file throughout. Is there any way to use the Desikan Atlas to "divide" say the lh.pial surface file and generate a number of .pial files each consisting of one of the regions described by the Desikan Atlas? Thanks, Zachary Humphrey

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vvol2surf flip issue
by Redwan Maatoug 11 Aug '17

11 Aug '17

Hi Doug, First of all sorry to bother you again with that. We still have an issue with the vol2surf command line and almost all the people in the lab tried without any success. We have the following nifti file attached and we tried to convert it to surface file. We used a MNI152 2mm brain template and when we look at the image with tksurfer, the image is flipped. (we have this issue with half of the data). I have attached the screenshot of the NIFTI file displayed with freeview. (file1) I have attached how we are supposed to see the MGH file (not flipped) in tksurfer I have attached how we see the MGH file (flipped) The command line we have used : *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152_T1_brain.dat --t1 --init-coreg* *mri_vol2surf --file1.nii --reg MNI152_T1_brain.dat --hemi rh --o file1.mgh* Can you try to replicate the issue or give some tips ? We have this issue with half of the data Thank you very much, I would really appreciate any help, Redwan

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Re: [Freesurfer] mri_glmfit-sim output
by Van Der Deijl, Rosanne 11 Aug '17

11 Aug '17

Thanks for the link, I hadn't seen that one indeed! However, the variable WghtVtx is not explained on this page. What is this variable? Thank you! Message: 8 Date: Mon, 7 Aug 2017 15:01:46 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] mri_glmfit-sim output To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <0b5fc464-a5ed-cee5-e3fa-3603b99e8136(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed see here https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisClusterSu… On 08/07/2017 02:40 PM, Van Der Deijl, Rosanne wrote: > Dear Freesurfer team, > > In the mri_glmfit-sim summary output file, I get a number of output > variables, and I'm not sure what some of them are. Could you explain > the ones in bold to me? > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ *CWP > CWPLow CWPH * NVtxs *WghtVtx* Annot > 1 2.015 134872 355.89 -36.3 -9.7 -1.4 > 0.96620 0.96390 0.96850 841 1298.68 insula > 2 1.652 71259 154.25 -49.4 -52.7 39.2 > 1.00000 -0.00010 1.00000 363 526.18 supramarginal > 3 -1.521 91550 39.92 -37.1 -26.5 -23.3 > 1.00000 -0.00010 1.00000 90 -125.33 fusiform > 4 1.322 139141 0.76 -36.4 3.5 -10.7 > 1.00000 -0.00010 1.00000 2 2.62 insula > 5 1.312 73658 0.47 -36.0 -4.4 9.6 > 1.00000 -0.00010 1.00000 1 1.31 insula > 6 1.387 133422 0.44 -5.1 -17.2 51.7 > 1.00000 -0.00010 1.00000 1 1.39 paracentral > > I know CWP stands for Cluster-wise P-value. But what is the low and > the high number, a confidence interval? And isn't it odd that my > p-values are (almost) 1? > > Thank you in advance. > > Kind regards, > > Rose >

2 1

Test-retest reliability small subcortical regions
by Van Der Deijl, Rosanne 11 Aug '17

11 Aug '17

Dear Freesurfer team, I was wondering what the test-retest reliability is of comparing small regions in the subcortical volume, e.g. the amygdala. Has this improved with the 6.0 version? Thank you! Kind regards, Rose

2 1

PET surfer
by John Anderson 11 Aug '17

11 Aug '17

Hi Dr Greve, I have PET data for two groups and I used PET surfer in FSV 6.0 to run the analyses. The pipeline is straightforward and the analysis ran smoothly without any issues. Is it correct procedure to adjust PET signal to differences in gray matter volume or cortical thinness between two groups? In other words, is it correct if gray matter volume or cortical thickness for subjects be included as EVs in GLM or a nausiance factor in QDEC? Specifically, is the PET signal changeable depending on differences in cortical thickness. or differences in gray matter volume? Thank you for any clarification > Thank you ! > Jon

2 4

(no subject)
by Redwan Maatoug 10 Aug '17

10 Aug '17

Hi Doug, First of all sorry to bother you again with that. We still have an issue with the mri_convert command line and almost all the people in the lab tried without any success. We have the following nifti file attached and we tried to convert it to surface file. We used a MNI152 2mm brain template and when we look at the image with tksurfer, the image is flipped. (we have this issue with half of the data). I have attached the screenshot of the NIFTI file displayed with freeview. (file1) I have attached how we are supposed to see the MGH file (not flipped) in tksurfer I have attached how we see tne MGH file (flipped) The command line we have used : *bbregister --s fsaverage --mov MNI152_T1_2mm_brain.nii --reg MNI152_T1_brain.dat --t1 --init-coreg* *mri_vol2surf --file1.nii --reg MNI152_T1_brain.dat --hemi rh --o file1.mgh* I have attached one of the nifti file to see if you can replicate the issue. Thank you very much, I would really appreciate any help, Redwan

1 0

"failed to load mri" in terminal, not in GUI
by Z Hessam 10 Aug '17

10 Aug '17

Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards

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mri_surf2vol
by Rockers, Elijah D. 10 Aug '17

10 Aug '17

I am attempting to create a volume from a surface. My ultimate goal is to obtain a mask that includes everything "inside" the white matter surfaces. wm.mgz is close, but it would nicer to just get a mask from lh.white and rh.white. I would like these masks to be in the subject's native space. However I try the following command and see the resulting error: mri_surf2vol --o coleMRI06162006/mri/lh.white.mask.mgz --mkmask --hemi lh --identity coleMRI06162006 --template coleMRI06162006/mri/orig/orig.mgz gdiagno = -1 Using identity matrix for registration mghRead(coleMRI06162006/mri/orig/orig.mgz, -1): could not open file mri_surf2vol ERROR: reading coleMRI06162006/mri/orig/orig.mgz header I'm obviously doing something wrong here, but I'm not sure what needs to change. I used --identity because native space, and it wouldn't let me run the command without specifying --template, which I'm not sure I understand, because, again, target is native space. Please illuminate me, Thank you, - 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 facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist 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

Talairach error
by Yagmur Ozdemir 19 10 Aug '17

10 Aug '17

Hello FreeSurfer experts, I have been running into a consistent problem of Talairach alignment error in my recon-all for some of my subjects, even though I was able to get a completed recon-all for other subjects by using the same procedure to obtain my nifti files. I have attached the recon-all logs of a successful and a Talairach failed subject respectively, and as I try to understand the difference, in the successful one this was tried the last: INFO: Trying MINC mritotal to perform Talairach align... then failed, then there is a "New invocation of recon-all " which succeeded. I do not think I made that invocation. Could someone help me figure out what I am missing, and how can I make recon-all continue as I somehow did previously? Thank you so much! Idil

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mri_binarize command help
by Yagmur Ozdemir 19 10 Aug '17

10 Aug '17

Dear FreeSurfer experts, I am trying to use the following command to merge the volume file of a template with original T1 orientation*, with a file like rawavg to get the full brain volume, but the following attached image gets produced and I am pretty sure, as a freesurfer novice, I am using a wrong command line; mri_binarize --i rawavg.mgz --o scanner.template_angle.mgz --wm+vcsf * (I have the native oriented version of this volume template as well, and I attached a photo of the template as well) I would deeply appreciate if someone could help me correct my command line. Thank you all for the time and help Idil

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Freesurfer August 2017