Re: [Freesurfer] Multiple Comparisons Correction thresh error

Hello, I forgot to mention in my previous email that the system locale is in Swedish. Can this be the reason? Regards,Teodora On Thursday, April 6, 2017, 1:07:56 PM GMT+2, teodora petrova wrote:Hello, I would like to correct my glm_fit results for multiple

[Freesurfer] Custom registration template

Dear all, I've been following the instructions for building a custom registration template as written here ( http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) and here ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html ). I'm now at the mris_preproc

[Freesurfer] Error during recon-all

Dear FreeSurfer Developers, I was trying to use the command recon-all -autorecon1 -subjid bert and got an error. When I checked I found the error was coming while executing the below command: nu_correct -clobber ./tmp.mri_nu_correct.mni.7555/nu0.mnc ./tmp.mri_nu_correct.mni.7555/nu1.mnc

[Freesurfer] recon-all -parallel osx sierra

Dear all, I am using Freesurfer 6.0 to run recon-all on 0.8 isotropic data. Whenever I use the parallel flag I get this error. dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Same subject without the parallel flag runs smoothly but of course takes much longer. I have

Re: [Freesurfer] help

Use mri_binarize --i aseg.mgz --match 17 --binval -1 --o your.lefthippo.nii.gz On 4/6/17 6:00 AM, Dilip Puri wrote: Hi everyone, I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images. I am using

[Freesurfer] First-level GLM on externally-preprocessed functionals

Hi list, We're working on making a preprocessing stream that will be generally accessible to different analysis streams, including FreeSurfer. One component of this is sampling functional volumes to FreeSurfer meshes, and I want to test this component by running a simple first-level GLM in

Re: [Freesurfer] R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

yes, those are the residuals On 4/5/17 5:39 PM, std...@virgilio.it wrote: Hi, as you advise I have run selxavg3-sess with the -svres option. I found a folder called "res" which contain "res-001.nii". Is it the f.nii fully processed? Thanks Stefano Messaggio originale Da:

Re: [Freesurfer] Re. display SPM results on inflated surface? {Disarmed}

I got it from FSL in the $FSLDIR/data/standard, but it is distributed with SPM as well On 4/5/17 9:39 PM, Kevin Aquino wrote: Hi Douglas, I am wondering, where did you find the mini 152 T1 map? :) Regarding this... Would it be better to instead run recon-all on a higher-res MNI atlas? and

Re: [Freesurfer] Multiple Comparisons Correction thresh error

I think this is a "language" problem in that it is converting the "1.3" into "1,3" and then getting confused. I'm not sure how to fix it, but I think it has to do with the LOCAL setting. On 4/6/17 5:07 AM, teodora petrova wrote: Hello, I would like to correct my glm_fit results for multiple

Re: [Freesurfer] How to generate binary mask image using FreeSurfer's “mri_volsynth”?

It should save it in the current directory. But I don't think we write out IMA files. Why not use nifti (nii or nii.gz)? On 4/5/17 2:05 PM, Karan Vahi wrote: Dear Freesurfers, I am trying to implement the methods mentioned in this paper to deal with partial volume effects when quantifying

Re: [Freesurfer] R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

It will be in the space that you analyzed it in. If you want the native space, then use -native when running preproc-sess and mkanalysis On 4/6/17 2:34 AM, std...@virgilio.it wrote: Furthermore, the res-001.nii which is produce in produced in the res folder in not the same dimension of f.nii.

[Freesurfer] postdoctoral Research Fellow position at Mayo Clinic

The Mayo Clinic Departments of Neurology and Diagnostic Radiology in Rochester, Minnesota are seeking applications for a fully-funded, two-year postdoctoral Research Fellow position to begin in July of 2017. The Research Fellow position will primarily work on developing advanced multi-modal

Re: [Freesurfer] Custom color maps

hi, I've read through the list, and searched over the last few days, and can't quite seem to find what I'm looking for. My first message wasn't clear at all either (my apologies), it was one of those days where your brain ends up in a bit of a fog. I am trying to get a heat map style visual

Re: [Freesurfer] long mri_ca_register error

Hi Chris it's possible we never looked at -bigventricle in the long stage. What was your recon-all command line? cheers Bruce On Thu, 6 Apr 2017, Chris Adamson wrote: It happens when I use -bigventricles.   From: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] help

Hi Dilip yes, freesurfer will do this for you, although the labels will be 17 for left hippocampus and 53 for right. cheers Bruce On Thu, 6 Apr 2017, Dilip Puri wrote: > Hi everyone, > > I am working on Hippocampus segmentation using Neural Networks for that I > need labeled images of

Re: [Freesurfer] MRIread (load_nifti)- Out of memory

Hi Ilaria do you have any reason to believe that it isn't just out of memory? If so, there's not much to do other than get more RAM or use a different machine cheers Bruce On Thu, 6 Apr 2017, Ilaria Sani wrote: Dear All,   I’m trying to load a pretty big diffusion MRI dataset

Re: [Freesurfer] MRIread (load_nifti)- Out of memory

is it a compressed nifti (nii.gz)? If so, try uncompressing it first On 04/06/2017 02:53 PM, Ilaria Sani wrote: > Hi Bruce, > > Not sure this answer your question... > > In matlab workspace, I am able to load data in two halves: > > H1=MRIread(half1) > H2=MRIread(half2) > > And then concatenate

Re: [Freesurfer] Custom color maps

Thanks, I'll take a look at it and let you know how it goes. Peter From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, April 06, 2017 1:00 PM To:

Re: [Freesurfer] First-level GLM on externally-preprocessed functionals

You should be able to do it that way. When you run mkanalysis, specify -funcstem fmcpr.sm0.fsaverage.lh.nii.gz, and then selxavg3-sess will then use that file as input. If you want to smooth, then do that explicitly and pass the smoothed file to mkanalysis On 04/06/2017 12:35 PM, Christopher

Re: [Freesurfer] Custom registration template

1. The "..." means to include the other options needed for the command to run. Looks like you figured it out. Using -f as you have is correct. 2. can you send the full terminal output? On 04/06/2017 08:55 AM, Linda Zhang wrote: > Dear all, > > I've been following the instructions for building

Re: [Freesurfer] General QDEC clarification queastions

On 04/03/2017 01:45 PM, Veggeberg, Rosanna wrote: > Hello, > I am using QDEC to analyze cortical structural data and am looking for > some clarification on some questions that have come up. > > 1. _Design tab_: In the "Measure" drop-down selection, I understand > what we are getting when

Re: [Freesurfer] MRIread (load_nifti)- Out of memory

Hi Bruce, Not sure this answer your question... In matlab workspace, I am able to load data in two halves: H1=MRIread(half1) H2=MRIread(half2) And then concatenate the volumes concatenate them var=cat(4,H1,H2). So, somehow matlab can handle... However, when those operations are embedded

Re: [Freesurfer] Ventricle-to-Brain Ratio

that looks right. how different are the values? On 04/05/2017 10:58 AM, Gullickson, James wrote: > Hello all, > > I want to calculate a Ventricle-to-Brain ratio (VBR) as a measure of > parenchymal atrophy using Freesurfer version 5.3.0. I have tried to go > about this using the aseg.stats

Re: [Freesurfer] QDEC-volume, thickness and area

what do you mean they do not differ in gender ratio? Just that the relative number of M/F is the same in each group? If there is not a significant interaction between gender and group, then you can usually merge the genders. On 04/05/2017 05:13 PM, Lim, Lena wrote: > > Dear Freesurfer

Re: [Freesurfer] Custom color maps

See if annotval2surfoverlay.m does what you want. It is in v6. If you have v5.x, I can send you the mfile separtely On 04/06/2017 01:00 PM, Senften, Peter wrote: > hi, > > I've read through the list, and searched over the last few days, and can't > quite seem to find what I'm looking for. My

Re: [Freesurfer] Selxavg3-sess Looking for (and can't find) "fmc.sm0"

can you send the full terminal output? On 04/05/2017 04:02 PM, Taylor, Johnmark wrote: > Hello, > > I am getting an odd bug on selxavg3-sess. I am getting the error message, > > *ERROR: cannot find [rest of file path]/fmc.sm0* > > I am indicating zero smoothing in mkanalysis-sess ("-fwhm 0"). I

Re: [Freesurfer] ROI seed size

these are good questions without good answers. It is hard to compare surface-based vs volume-based. The surface-based may be smaller, but it will only include gray matter whereas a volume-based sphere will be bigger but will include WM and CSF. If you're voxel size is small, then 3mm radius

Re: [Freesurfer] correlation coefficient R

I guess you could average it over space (eg, over a cluster). Let me know if you want instructions. Otherwise, I'm not sure what to say. On 04/04/2017 06:49 AM, tom parker wrote: > Hi Doug, > Thanks! I realize now I didn't explain myself properly. > I need one single R value for the correlation

[Freesurfer] QDEC and ROI drawing

Dear Freesurfer's experts, I draw a specific region on fsaverage using QDEC, then I mapped this label on each subject using mri_label2label. I looked at these registered labels using freeview. Most of them are perfect but for some of them I would like to correct the segmentation. I would like to

[Freesurfer] R: Re: R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

Thanks.The file could not be open by fslview.I presume that it is inflated.How can I do to transform it?Stefano Messaggio originale Da: "Douglas Greve" Data: 6-apr-2017 17.56 A: Ogg: Re: [Freesurfer] R: R: Re: R: Re:

Re: [Freesurfer] QDEC and ROI drawing

what is your label2label command line? On 04/06/2017 04:52 PM, Arnaud Boré wrote: > Dear Freesurfer's experts, > I draw a specific region on fsaverage using QDEC, then I mapped this > label on each subject using mri_label2label. I looked at these > registered labels using freeview. Most of

Re: [Freesurfer] QDEC-volume, thickness and area

Thanks, Doug. There is no significant interaction and I merged the males and females within each group, but the reviewer wants me to include gender as a covariate. Do we always need to control for gender esp. when the group x gender is insignificant? Will that be "over-controlled"?

Re: [Freesurfer] Custom registration template

Hi Douglas, Thanks, good to know! That was the full terminal output after I ran mris_preproc, though. Cheers, Linda On Thu, 6 Apr 2017 at 22:07 Douglas N Greve wrote: > 1. The "..." means to include the other options needed for the command > to run. Looks like you

Re: [Freesurfer] QDEC-volume, thickness and area

probably so. It is up to you whether you want to fight the reviewer or not. On 04/06/2017 05:08 PM, Lim, Lena wrote: > > Thanks, Doug. > > > There is no significant interaction and I merged the males and females > within each group, but the reviewer wants me to include gender as a > covariate.

Re: [Freesurfer] R: Re: R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

depends on your analysis but probably so On 04/06/2017 05:26 PM, std...@virgilio.it wrote: > Thanks. > The file could not be open by fslview. > I presume that it is inflated. > How can I do to transform it? > Stefano > > Messaggio originale > Da: "Douglas Greve"

Re: [Freesurfer] Ventricle-to-Brain Ratio

Doug, Thanks for your reply. Difference between the two TVV methods ranges between 1-6% Difference between the two TBV methods ranges between 2-4% Basically, my question is two-fold: a) what is the most accurate representation of total ventricular volume b) what is the most accurate

[Freesurfer] QDEC-Cortical Thickness

Hello Freesurfer Experts, I want to compare the cortical thickness between the groups (HC & Patients), and wanted to know where qdec shows this information. Once the design tab is loaded, I am seeing the question in the analysis results – does the correlation between thickness and Age differ

Re: [Freesurfer] long mri_ca_register error

It happens when I use -bigventricles. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Chris Adamson Sent: Thursday, 6 April 2017 12:27 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] long mri_ca_register error Freesurfer

Re: [Freesurfer] Fwd: recon-all error

Dear Patricia, this is I suppose the last issue concerning symbolic links, related with part of code starting with following comment:  # if fsaverage is not in subjects dir, put it there I think that the most straightforward  solution of this issue is to manually copy the fsaverage subject to

Re: [Freesurfer] Fwd: recon-all error

Hi Antonin, I edited recon-all file, but another error was reported. This error concerns symbolic links, too. Is there any way I could make it work on this virtual machine? I coud try to substitute all ln commands with cp or something like that. Thanks. Patricia 2017-04-04 13:43 GMT+02:00

[Freesurfer] QA Tools v1.2 and future release

Dear Freesurfer Experts, As one of the new freesurfers, I really appreciate the excellent work of authors as well as great support of users' forum. A good guess of mine is that authors, e.g., Vasanth or Louis etc., are busy updating QA tools after the FSv6 release since the QA Tools v1.2 was

[Freesurfer] help

Hi everyone, I am working on Hippocampus segmentation using Neural Networks for that I need labeled images of Hippocampus corresponding to original images. I am using OASIS Dataset for this. I want to generate labeled images using FREESURFER. Is there any way to label each 3D co-ordinate

[Freesurfer] Multiple Comparisons Correction thresh error

Hello, I would like to correct my glm_fit results for multiple comparisons. I am using the following commands, similar to the one in the group analysis tutorial: mri_glmfit-sim  --glmdir lh.index.glmdir  --cache 1.3 abs  --cwp 0.05  --2spacesmri_glmfit-sim  --glmdir lh.index.glmdir  --cache

Re: [Freesurfer] long mri_ca_register error

Just the standard pipeline. recon-all -s cross1 -all -bigventricles recon-all -base cross -tp cross1 ... -all -bigventricles recon-all -long cross1 cross -all -bigventricles -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]

Re: [Freesurfer] MRIread (load_nifti)- Out of memory

Hi Doug, Thanks for the tip. I can load the volume now! I'm getting different types of errors when I proceed with my analyses though. Can you help me to understand why it works when data are decompressed and in what way data are different now. Thanks a lot, Ilaria -Original Message-

Re: [Freesurfer] help

Hi everyone, when I used following command: mri_binarize --i myfile.img --match 17 --binval -1 --o your.lefthippo.nii.gz then I got output your.lefthippo.nii.gz file when I read this file using FREEVIEW then it completly different from original mask. Thanks Dilip​ On Thu, Apr 6, 2017 at

[Freesurfer] R: R: Re: R: Re: Whole preprocessing with FAST without to perform a seed based analysis

Furthermore, the res-001.nii which is produce in produced in the res folder in not the same dimension of f.nii.I would do the whole FAST preprocessing on f.nii., maintaining the same dimension and open it with FSL.ThanksStefano Messaggio originale Da: std...@virgilio.it Data: