[Freesurfer] Rat model in FreeSurfer

Hi, one of our lab mates who works with small animal models would also like to try FreeSurfer. I know from the mail archive that people have used it like this before. Could any people that have used it on rats please give some info on what they have tried? Cheers, Melanie -- Melanie Ganz-

Re: [Freesurfer] recon-all on 0.5mm scan?

Hi Trisanna, you can find instructions on how to process data with an isotropic resolution other than 1mm^3 with FreeSurfer v5.1 and above here: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon For v5.3 the pipeline should be slightly adapted, however, can easily be done. If you need assist

[Freesurfer] glmdir question

Dear FreeSurfer Experts, when running the Monte Carlo correction on a GLM I specify this command: mri_glmfit-sim --glmdir lh.gender_age.glmdir --cache 4 neg --cwp 0.05 --2spaces This assumes that my mgh file that I used as input for the GLM is in lh.gender_age.glmdir. That means though, that e

Re: [Freesurfer] New to Freesurfer; cortical thickness

Hi Marja can you send us the actual command and screen output you ran? It should be something like: recon-all -all -s -i Depending on your hardware it will take hours to finish, but it will do pretty much everything (segmentation, surface reconstruction, template registration, thickness m

[Freesurfer] mri_glmfit version

Dear FS experts We have been playing around with different mri_glmfit versions. I processed all my data with FS v5.1, and then I run the mri_glmfit with both the 5.1 and 5.3 versions, using exactly the same X, same contrasts matrix and obviously the same images. Our concern is that the results dif

Re: [Freesurfer] New to Freesurfer; cortical thickness

Hi Bruce, Thank you for your response. I tried it many times and I kept getting the same error like at the bottom of this email. Why do you put the -s in there? and what exactly is the subject ID? FYI, I was already in the folder where the .nii.gz is located. And by your answer I assume I can do

[Freesurfer] Cluster-wise correction error with mri_glmfit-sim

Hello: Freesurfers, follow the tutorial ' * FsTutorial * GroupAnalysis', my task is to fi

Re: [Freesurfer] New to Freesurfer; cortical thickness

the subject id is something you make up. What is 001 in your example? Maybe it is the subject ID? If so, preface it with -s. You probably also want to specify the location of your output directory with -sd where you will put each subject> cheers Bruce On Fri, 27 May 2016, Marja Caverlé wrote:

Re: [Freesurfer] New to Freesurfer; cortical thickness

Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put? Best, Marja On Fri, May 27, 2016 at 12:41 AM, Bruce Fischl wrote: > the subject id is something you make up. What is 001 in your example? > Maybe it is

Re: [Freesurfer] New to Freesurfer; cortical thickness

Thanks! It runs now. But that still leaves me with the question whether I can do all the patients in one run or that I have to run them separately. Best, Marja On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé wrote: > Thanks Bruce, > > 001 was indeed the subject id, but I did not know it needed

Re: [Freesurfer] New to Freesurfer; cortical thickness

run them separately On 5/26/16 11:01 AM, Marja Caverlé wrote: Thanks! It runs now. But that still leaves me with the question whether I can do all the patients in one run or that I have to run them separately. Best, Marja On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé mailto:marja.cave...

Re: [Freesurfer] New to Freesurfer; cortical thickness

Thanks Douglas! On Fri, May 27, 2016 at 1:02 AM, Douglas Greve wrote: > run them separately > > On 5/26/16 11:01 AM, Marja Caverlé wrote: > > Thanks! It runs now. But that still leaves me with the question whether I > can do all the patients in one run or that I have to run them separately. > >

Re: [Freesurfer] Cluster-wise correction error with mri_glmfit-sim

Instead of --2spaces, use--bonferroni 2 On 5/26/16 10:30 AM, Hao wen wrote: Hello: Freesurfers, follow the tutorial ' # FsTutorial # GroupAnalysis

Re: [Freesurfer] request for corrected p-values for mni305 space

What do you mean? There is a way to correct with mri_glmfit-sim using the --grf option. On 5/25/16 9:25 PM, Joseph Dien wrote: Hi, just a user request for corrected p-values for the mni305 space analyses (i.e., sig.voxel.nii.gz files). Thanks! Joe ---

Re: [Freesurfer] New to Freesurfer; cortical thickness

If you don't give it a -s option, the program will not run and there will not be any output On 5/26/16 10:43 AM, Marja Caverlé wrote: Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put? Best, Marja On F

Re: [Freesurfer] New to Freesurfer; cortical thickness

whatever then environment variable SUBJECTS_DIR points to On Fri, 27 May 2016, Marja Caverlé wrote: Thanks Bruce, 001 was indeed the subject id, but I did not know it needed -s. If I don't specify the output directory, where will it be put? Best, Marja On Fri, May 27, 2016 at 12:41 AM, Bru

Re: [Freesurfer] New to Freesurfer; cortical thickness

you have to run them separately On Fri, 27 May 2016, Marja Caverlé wrote: Thanks! It runs now. But that still leaves me with the question whether I can do all the patients in one run or that I have to run them separately. Best, Marja On Fri, May 27, 2016 at 12:43 AM, Marja Caverlé wrote:

Re: [Freesurfer] glmdir question

What is it doing in your glmdir? Usually you'd have it in another location when running mri_glmfit (which creates the glmdir). In any case, you can run it with --no-y and it will not look for the input file (and will not compute means over the clusters). On 5/26/16 8:56 AM, Clara Kühn wrote: >

Re: [Freesurfer] glmdir question

I thought it had to be there because when I don't copy it into the glmdir I get an error message that it can't find the mgh in said glmdir. I'm gonna try running it with the flag you mentioned. What does it mean, though, that it won't compute means over the clusters? - Ursprüngliche Mail ---

[Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim

Doug: Thank you for your reply, it does not work, also, I think the problem is that for me after the clusterwise correction, I got no corrected cluster, I am not sure if it the problem that I set the --cache value and the --cwp value, but I changed the value, it always return me nothing! This

Re: [Freesurfer] 答复: Cluster-wise correction error with mri_glmfit-sim

It looks like it worked. there is not an error there. It did not find any voxels above your chosen level of signficance, but that is not an error per se On 05/26/2016 11:19 AM, Hao wen wrote: > > Doug: > > Thank you for your reply, it does not work, also, I think the problem > is that for me af

Re: [Freesurfer] glmdir question

By default it will compute a table. The rows of the table are each subject. The columns are the clusters. Each cell is the mean of the input for that subject over that cluster. It needs the input data to do this. On 05/26/2016 11:18 AM, Clara Kühn wrote: > I thought it had to be there because w

Re: [Freesurfer] Connectivity design ill-conditioned

It is strange that it has 47 columns, I would have expected 48, however, the current problem is caused by the wm.dat and vcsf.dat having the same content. Probably it was an error when you set up the command line for fcseed-config On 05/25/2016 06:40 PM, Zimmerman, Jared Perry wrote: > Hi, I'

Re: [Freesurfer] mri_glmfit version

I don't know of any difference that would have caused this, though it has been a long time since 5.1. The 0.3 shift is suspicious because that is the difference between a signed test and an unsigned test in log10(p). Can you capture the screen output from the two runs and send them to me? On

[Freesurfer] 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

Hi, I tried every value for the --cache and --cwp, as what i understood, the --cache is the threshold for the vertex-wise correction and the --cwp is the clusterwise correction, and i even tried the 0.99 with the --cwp, which should give me all my cluster, but still, I got nothing, I checked the

Re: [Freesurfer] 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

why do you think there shold be a cluster? On 05/26/2016 12:21 PM, Hao wen wrote: > Hi, > I tried every value for the --cache and --cwp, as what i understood, the > --cache is the threshold for the vertex-wise correction and the --cwp is the > clusterwise correction, and i even tried the 0.99 wi

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

Please send the design matrix On 05/24/2016 08:05 PM, Hanbyul Cho wrote: > Dear Douglas N Greve, > > Today, I tested the previous group analysis on other computer, and saw > the same error massage. > > I attached the tested fsgd and mtx files. > > command: > mri_glmfit --y 052416_lh.Pa_Co_G2V2_do

[Freesurfer] (no subject)

Hello, As we know, Freesurfer generates separate surface models and associated labels for each brain hemisphere, is there any way to merge two hemisphere and come up with a single cortex surface? My best, Saeed ___ Freesurfer mailing list Freesurfer@nmr

Re: [Freesurfer] glmdir question

Hi Doug, I ran this command with the --no-y Flag: mri_glmfit-sim --glmdir $SUBJECTS_DIR/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thick10_groupcontrasts_sc1.glmdir --cache-dir $SUBJECTS_DIR/average/mult-comp-cor --cache 3.0 abs --cwp 0.05 --2spaces --no-y and got the following err

Re: [Freesurfer] glmdir question

Try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim On 05/26/2016 12:53 PM, Clara Kühn wrote: > Hi Doug, > > I ran this command with the --no-y Flag: > > mri_glmfit-sim --glmdir > $SUBJECTS_DIR/qdec/87kids/2016.05.26_glm_groupscontrasts/87kids_lh.thic

Re: [Freesurfer] Design Matrix Creation

Hi Doug, Thank you for such a prompt response. Just to be clear you are recommending that I manually create the matrix file right? If so I want to ensure that I am understanding how to design the matrix file properly. Let's imagine that the first participant is a control and is 13 and the second

Re: [Freesurfer] Design Matrix Creation

Yes, create your matrix manually. Those matrix lines are not quite right. The ages are in the correct column, but you need a 1 somewhere in columns 1-8 to indicate the class (ie, site/dx) that the subject is in. On 05/26/2016 12:57 PM, Timothy Hendrickson wrote: > Hi Doug, > > Thank you for suc

[Freesurfer] 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

Hi: Because I make the group analysis with SurfStat, and I get the cluster after the clusterwise correction, so I think in Freesurfer, we should have the similiar result:) 发件人: freesurfer-boun...@nmr.mgh.harvard.edu 代表 Douglas N Greve 发送时间: 2016年5月26日

Re: [Freesurfer] 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

They use two different methods. SurfStat uses gaussian random fields and FS uses monte carlo simulation. How significant is your cluster in FS? On 05/26/2016 01:17 PM, Hao wen wrote: > Hi: > Because I make the group analysis with SurfStat, and I get the cluster after > the clusterwise correction

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

Dear Douglas N Greve, The Contrast matrix was = [1 -1 0 0 0 0] I attached the Xg.dat printed by unended mri_glmfit process. Thank you. Han. On Thu, May 26, 2016 at 10:37 AM, Douglas N Greve wrote: > Please send the design matrix > > On 05/24/2016 08:05 PM, Hanbyul Cho wrote: > > Dear Douglas

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

Design matrix, not contrast matrix. It was printed out as part of the terminal output. It can also be found in glmdir/Xg.dat On 05/26/2016 01:48 PM, Hanbyul Cho wrote: > Dear Douglas N Greve, > > The Contrast matrix was = [1 -1 0 0 0 0] > I attached the Xg.dat printed by unended mri_glmfit proces

Re: [Freesurfer] Group Analysis: Two Groups and Two Covariates.

Dear Douglas N Greve, I sent again this design matrix (= Xg.dat) by attached. Thank you. Han. On Thu, May 26, 2016 at 11:59 AM, Douglas N Greve wrote: > Design matrix, not contrast matrix. It was printed out as part of the > terminal output. It can also be found in glmdir/Xg.dat > > On 05/26

[Freesurfer] 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

Hi, Doug: I find something, here r my command: mri_glmfit-sim \ --glmdir lh.AD_CN_NO_COVARIATE.glmdir \ --cache 4 pos \ --cwp 0.05 so I changed the sign, at first, it was 'neg', after correction, i got no cluster, but with 'pos', I got Ncluster = 9, and with 'abs', I got Ncluster = 8, S

Re: [Freesurfer] 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

the sign is the expected sign of the contrast. If you do not have an apriori expectation as to what the sign is, then use abs (an unsigned test). Probably SurfStat uses pos. 4 = -log10(pthresh) sets the voxel-wise (ie, cluster forming threshold). You probably have to set a z-threshold for SurfS

[Freesurfer] 答复: 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

Hi, Doug: I check out the documentation for this command: 'mri_surfcluster', and I also played with another comparision, with the --cache value with 1.3 and 4, and I get fewer cluster with 1.3, so right now I got the idea for the --cache value, but Im still confused about how do you decide which

Re: [Freesurfer] 答复: 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

That depends on what you expect from your data. If you do not have an apriori hypothesis about the sign of the contrast you are testing, then use abs (unsigned). Eg, if your hypothesis is Controls have a thicker cortex than ADs and you set up your contrast to be gamma = ThicknessControls - Thic

Re: [Freesurfer] LME MATLAB, X matrix error

Dear Martin Reuter, Thank you for your clear explanation. Best wishes, Han. On Tue, May 24, 2016 at 12:41 PM, Martin Reuter wrote: > Dear Han, > > if controls have only 1 time point, you cannot compare/analyse any > measurement of change across the groups (such as atrophy rates). You can > on

[Freesurfer] Merging Brain Hemispheres

Hello, As we know, Freesurfer generates separate surface models and associated labels for each brain hemisphere, is there any way to merge two hemisphere and come up with a single cortex surface? My best, Saeed ___ Freesurfer mailing list Freesurfer@nm

[Freesurfer] Segmentation of a 3D IR-deskulled volume

Dear Freesurfer team, I'm trying to segment a brain from a non standard sequence. It is a 3D IR sequence that I have previously pre-elaborated and deskulled. The software is running from a long time and at the moment is correcting defects (17/128) but I'm not sure it's working properly. I ha

Re: [Freesurfer] 答复: 答复: 答复: 答复: 答复: Cluster-wise correction error with mri_glmfit-sim

Thanks very much, right now, I am clear! De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Douglas N Greve Envoyé : jeudi 26 mai 2016 21:14:28 À : freesurfer@nmr.mgh.harvard.edu Objet : Re: [Freesurfer] 答复: 答复: 答复: 答复: 答复: Cluster-wise correcti

Re: [Freesurfer] mris_preproc - srcsubjreg

Hi Doug, still wondering about this - thanks! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Makaretz, Sara Johanna [smakar...@mgh.harvard.edu] Sent: Tuesday, May 24, 2016 16:23 To: Freesurfer support li

Re: [Freesurfer] Coordinates in TRACULA group analysis

Hi Anastasia, Thank you for your answer. There aren't stats/*.path.mean.txt files and terminal says 'Could not read /Applications/freesurfer/subjects/cvs_avg35.' I checked /Application/freesurfer/subjects/cvs_avg35 folder and couldn't find COR-.info file. Could you tell me any resolutions, please?

[Freesurfer] roi mask?

Hi all, So I ran a recon-all -all on one of my subjects, and it completed without errors (according to the log). Now I would like to get cortical thickness numbers from this subject, but when I open the tutorial regarding this, it says it assumes that you already have a roi mask and a T1 in the sa