[Freesurfer] FLAIR registration

Hi all, We're trying to use FLAIR images in our recon-all pipeline. For half of the participants there are no problems using: recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FLAIR.nii -FLAIRpial However for the other half the FLAIR registrations are either a bit off or completely flipped, inclu

[Freesurfer] Variations in results between qdec GUI and Command Line

Dear Freesurfer Team, I am facing a discrepancy in the result when I run a Monte Carlo Z simulation. I have a group with 3 levels(normal,Non-psychotic and psychotic).I tried running an analysis to c the variation in cortical thickness between the same groups in the QDEC GUI,but since iit was impos

Re: [Freesurfer] Use of gcs altlas with freesurfer on T1 image

Dear, Thank you for all your advice. I have a last question, at the end of the process I have two different volumes containing the right and the left hemisphere parcellation. How can I combine these two parcellation to get one whole brain parcellation? Thank you, have a nice day. Yours faithfully

Re: [Freesurfer] Ris: eTIV question

Hi Angela gyrification is the ratio of areas and hence dimensionless, so I would think it wouldn't be much affected by TIV. cheers Bruce On Sun, 21 Feb 2016, angela.fav...@unipd.it wrote: In the case of a gyrification analysis, does correction for total brain volume make sense? Angela In

Re: [Freesurfer] FLAIR registration

can you try --init-spm instead of --init-fsl and see if it does better? On Mon, 22 Feb 2016, K. Wagstyl wrote: > Hi all, > > We're trying to use FLAIR images in our recon-all pipeline. For half of > the participants there are no problems using: > recon-all -subjid SUBJECT -i T1.nii -all -FLAIR FL

Re: [Freesurfer] FLAIR registration

Hi Bruce, --init-spm works much better thanks. Is there a way to rerun autorecon3 using --init-spm rather than --init-fsl? Or do we need to run the commands line by line. Cheers, Konrad On 2016-02-22 13:45, Bruce Fischl wrote: > can you try --init-spm instead of --init-fsl and see if it does b

Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

Hi, Just wanted to check and see if the following is an appropriate set-up for a repeated measures ANOVA. Thanks, Afsana __ Afsana Afzal Clinical Research Coordinator Massachusetts General Hospital Division of Neurotherapeutics Department of Psychiatry: Neurosciences

Re: [Freesurfer] FLAIR registration

not sure. Doug? On Mon, 22 Feb 2016, K. Wagstyl wrote: > Hi Bruce, > > --init-spm works much better thanks. Is there a way to rerun autorecon3 > using --init-spm rather than --init-fsl? > > Or do we need to run the commands line by line. > > Cheers, > Konrad > > On 2016-02-22 13:45, Bruce Fischl w

Re: [Freesurfer] longitudinal analysis Repeated Measures ANOVA 2x2

Dear FS Experts, I have followed the steps for doing a Repeated Measures ANOVA 2x2 in Freesurfer https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova also following the previous post: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-October/026287.html .

Re: [Freesurfer] qdec

Not sure. Can you run it separately for each subject? I suspect that there might be a subject with a bad stats file On 02/19/2016 02:58 PM, levi solomyak wrote: > Hi Douglas, > > Sure! Below is the terminal outputs when I try and run the command you > suggested on the first five subjects. Any he

Re: [Freesurfer] comparison between two hemisphere in single

On 02/20/2016 05:47 AM, Ashkan Faghiri wrote: > Thank you doug for you answer. > > So now I have two other question. > 1- how can I check the inter hemisphere registration quality? e.g. can > I check if the parcellation for the two hemisphere are matched well? > or there is other ways? You can

Re: [Freesurfer] Reference about: MeanCurv, GausCurv, FoldInd, CurvInd?

http://brainvis.wustl.edu/wiki/index.php/Folding/Measurements On 02/20/2016 01:22 PM, Bruce Fischl wrote: > Hi Marta > > A 2D surface (like the cortical white or pial models) has two > principal curvatures at each point - one in the direction of maximum > curvature and one in the direction of

[Freesurfer] Multiple Frames Error

Hi freesurfers, I am trying to run the recon-all command on a T1 weighted structural image for one of my subjects and I keep getting this error "Checking for (invalid) multi-frame inputs... ERROR: input(s) cannot have multiple frames! /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri

Re: [Freesurfer] Multiple Frames Error

Each input file should have one frame. What sequence did you run on the scanner? This usually happens when someone collected a multiecho mprage. If so, then compute the rms of the multiple echoes and run recon-all on that On 02/22/2016 11:29 AM, Marissa Pifer wrote: > Hi freesurfers, > > I am t

Re: [Freesurfer] Use of gcs altlas with freesurfer on T1 image

you can use mri_aparc2aseg. Look in the recon-all.log file for an example command line. On 02/22/2016 07:33 AM, Thomas Jacquemont wrote: > Dear, > > Thank you for all your advice. I have a last question, at the end of the > process I have two different volumes containing the right and the left >

Re: [Freesurfer] Longitudinal results questions

Hi Seth, I assume the image you send shows the surfaces of the two time point taken from the *.long.baseid directories (and not from the cross sectionally processed directories)? There are many reasons why surfaces are different across time points. Some include - motion artifacts in one time p

[Freesurfer] nu correct crash

Hi Angela, this does not seem to be related to longitudinal processing, your commands are OK. For some reason the nu_correct crashes (I changed the subject line). I don't know what causes that, maybe someone else has an idea. You have enough disk space? I copy the part from the log here: It

Re: [Freesurfer] mris_make_surfaces dimensions error

Hi Bruce, I checked and it is indeed a volume file with 256x256x256 size. The full command line was: mris_make_surfaces -cover_seg edited_ribbon.mgz subject_id lh Thanks Corinna On Sat, Feb 20, 2016 at 1:38 PM, Bruce Fischl wrote: > Hi Corinna > > can you send us your full command line? Sound

Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

I'm having a hard time deciphering what you are doing. Is this a functional study? What are the 5 classes? Why are there all 1s regardless of risk or reward level? On 02/19/2016 10:52 AM, Afzal, Afsana wrote: > Hi, > > I'm analyzing a decision making task with a 3x3 condition matrix: > pairings

Re: [Freesurfer] Variations in results between qdec GUI and Command Line

Hi Vikas, I can't quite understand what the problem is. Is it that the direction of the effect is not what you expect? That would have nothing to do with the correction for multiple comparisons. If you were not able to run in QDEC, what does the subject line of the email mean? doug On 02/22/201

Re: [Freesurfer] Multiple Frames Error

Hi Marissa why does it have multiple frames? What kind of acquisition was it? If you know which frame is the correct one you can always extract it, for example cd /Users/marchaut/Documents/myprojects/SOARmaster/SOAR26-1/mri/orig mv 001.mgz two_frames.mgz mri_convert -nth 0 two_frames.mgz 001.

Re: [Freesurfer] mris_make_surfaces dimensions error

can you send the full screen output also? On Mon, 22 Feb 2016, Corinna Bauer wrote: Hi Bruce, I checked and it is indeed a volume file with 256x256x256 size. The full command line was: mris_make_surfaces -cover_seg edited_ribbon.mgz subject_id lh Thanks Corinna On Sat, Feb 20, 2016 at 1:3

Re: [Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview) (Z K)

Dear Zeke, This is the output: "Mon Feb 22 18:27:05 CET 2016 /usr/local/freesurfer/subjects/myscan /usr/local/freesurfer/bin/recon-all -s myscan -i myscan.nii.gz subjid myscan setenv SUBJECTS_DIR /usr/local/freesurfer/subjects FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/loca

Re: [Freesurfer] mri_convert Ubuntu 14.04 LTS not working (neither is freeview) (Z K)

I suspect its failing because the data file is zipped. Try unzipping it first, then run the recon: $> gunzip myscan.nii.gz $> /usr/local/freesurfer/bin/recon-all -s myscan -i myscan.nii.gz If that does not work please upload the data and I will take a look. https://surfer.nmr.mgh.harva

Re: [Freesurfer] eTIV question

My experience with eTIV is that it's great with a perfect Talairach transform but otherwise is less accurate than other measures. Manually fixing the transforms and reprocessing as necessary will result in great eTIVs but requires quite a bit of manual work. What we do instead is just use the brai

Re: [Freesurfer] [FreeSurfer] Repeated Measures ANOVA in FSFAST

Hi, Sorry about the lack of clarification. Yes, it's a functional study. Each of the classes is a subject. I basically want to compute the main effect of risk at the group level (i.e. High Risk minus Low Risk) but there are multiple observations per risk level since there are three different

Re: [Freesurfer] Multiple Frames Error

Bruce, I'm not sure why it has multiple frames. It was a spin echo, T1 weighted structural MRI. I input the command you suggested and recon-all is running now. Thank you for your help! Marissa On Mon, Feb 22, 2016 at 12:24 PM, Bruce Fischl wrote: > Hi Marissa > > why does it have multiple fra

Re: [Freesurfer] qdec

Hi Douglas, I get the same error for every subject individually. I'm guessing there is a problem with my aseg.stats files but when I look through them they look okay to me. What would be the best way to identify the problem? Thank you! LS On Mon, Feb 22, 2016 at 11:18 AM, Douglas N Greve wrote:

Re: [Freesurfer] qdec

can you send one of them? On 02/22/2016 03:13 PM, levi solomyak wrote: > Hi Douglas, > > I get the same error for every subject individually. I'm guessing > there is a problem with my aseg.stats files but when I look through > them they look okay to me. What would be the best way to identify the

Re: [Freesurfer] Multiple Frames Error

But is that the right frame to use? I would check with whoever collected the data and get it sorted out before diving into an analysis. On 02/22/2016 02:34 PM, Marissa Pifer wrote: > Bruce, > > I'm not sure why it has multiple frames. It was a spin echo, T1 > weighted structural MRI. I input the

Re: [Freesurfer] Multiple Frames Error

Absolutely, I've contacted them about it, and if it is not the right one, I can use the other. There are only 2 frames so I can narrow it down at least. Marissa On Mon, Feb 22, 2016 at 3:46 PM, Douglas N Greve wrote: > But is that the right frame to use? I would check with whoever collected > t

Re: [Freesurfer] Ris: eTIV question

Hi Bruce, this is true, but I noticed that many papers used TIV as a covariate. In addition, in my samples (both pathological and healthy) there is a moderate positive correlation between gyrification and TIV (and brain volume). For the hemispheric overall gyrification index the correlation is 0.3-

Re: [Freesurfer] Ris: eTIV question

Hi Angela yes, although if the eTIV is (incorrectly) correlated with atrophy you may be removing some of your effect (and slightly reducing your power) cheers Bruce On Mon, 22 Feb 2016, angela.fav...@unipd.it wrote: Hi Bruce, this is true, but I noticed that many papers used TIV as a covar

[Freesurfer] control points function

Hello, I am new to using Freesurfer and am currently using it for a biomedical image processing class. I am working on a project and would like to know the image processing technique behind the Control Points function. Is it region growing, or what other process? Thanks for the help! Kiersten ___

Re: [Freesurfer] bbregister problems

If you have spm, you can use --init-spm. Alternatively, you can use mri_coreg instead of bbr (bbr is not as effective on blurry data) ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg mri_coreg --s $fs --mov ${pet_ext}_LIA.nii --lta output.lta Also, why is the top of the

[Freesurfer] Read_surf error in reading "lh.seghead" head surface created from "mkheadsurf"

Dear FreeSurfer users, I have used the "mkheadsurf" function to create "lh.seghead" in the surf folder of my subject. Now I am trying to extract the vertices and faces of "lh.seghead" in the following way: *[vertex_coords, faces] = read_surf('lh.seghead')* but get an error in read_sur

Re: [Freesurfer] Ris: eTIV question

Even assuming one had a true measure of TIV, if you get meaningfully different results when using TIV vs. brain size as a covariate, isn’t that a rather important thing to point out? cheers, -MH -- Michael Harms, Ph.D. --- Conte Center for

Re: [Freesurfer] Ris: eTIV question

That is, going back to your earlier post, I personally don’t find it all that interesting whether a given brain area is atrophic relative to head size, especially in the situation where many regions are atrophic (i.e., global atrophy). I’m more interested in knowing whether the atrophy in a given