Re: [Freesurfer] cluster as ROI

Hi Doug, I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I also have a contrasts.sig.mgh file in the gmldir. Could either of these be used instead of csdbase.sig.ocn.mgh? Or how could I retrieve this file? Thanks for your help! Clara - Ursprüngliche Mail -

[Freesurfer] Freeview

Dear Experts, I load the T1 and aseg file in freeveiw and select the lookup table ,and show as isosurface in 3D view for a label .Is it possible to change the color(for example label 13 is blue but I want to show it as yellow!).another question is that if I want to show multiple labels which are

Re: [Freesurfer] Comparability of FreeSurfer segmentations across different MRI acquisition specs

Hi Darko what you are asking for is an unsolved problem in brain morphometry. We try very hard to be insensitive/adaptive to MR sequence, but depending on how big your acquisition differences are it is a very, very difficult problem. Do you have the sam esubject(s) scanned on the different

Re: [Freesurfer] Freeview

Hi Nazanin, To change color you will need to modify the look up table, i.e., load your own look up table. There is no way to only display a few selected labels. As a workaround, you may try applying a look up table with only a few labels in it. Best, Ruopeng > On Feb 21, 2017, at 5:20 AM, N

[Freesurfer] Comparability of FreeSurfer segmentations across different MRI acquisition specs

Hi, I’m doing volumetric analyses on MR structural data. The problem is that the scanning has been done on different MR machines, as well as with different sequences in some cases. This leads to different absolute values between subjects for volumes and thicknesses when being run through the

[Freesurfer] Nipype Workshop and Hackweek at MIT, March 27-31, 2017

The Nipype development team will be holding a workshop and hackweek at MIT, Cambridge, MA, USA, from March 27 - 31. For details and registration see: http://nipy.org/workshops/ 2017-03-boston/index.html cheers, satra ___ Freesurfer mailing list

[Freesurfer] -no-isrunning flag question

Hello, As I understand, adding the -no-isrunning flag will cause recon-all to ignore the 'isrunning.pial' file. I previously interrupted recon-all (while it was in the middle of a process) and I have now begun to re-run my subjects using this flag. I just wanted to check that any data

Re: [Freesurfer] mri_cvs_register error : PETSC Error

At the moment, unfortunately, not as the high resolution morphs are very large. Lilla On Mon, 20 Feb 2017, Bhavana Ganesh wrote: Hi Lilla, Is there a work around for this because I would at max be able to allocate 8GB for the tool but I dont have the resource for 35GB. Regards, Bhavana

[Freesurfer] mri_normalize 5.4 vs v6

Dear All, When I run mri_normalize on the same image using two freesurfer versions I get distorted results only on the V6. Can someone let me know how I can get the same results with V6? command: mri_normalize V5 output: voxel value range: 0 - 182 [image: Inline image 1] v6 output: voxel

Re: [Freesurfer] contrast matrix for one-way ANOVA with 1 factor, 4 groups

+Greve%22> Tue, 21 Feb 2017 12:53:08 -0800<http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu=date:20170221> That four group test will yield the same exact result as 1 -1 0 0 1 0 -1 0 1 0 0 -1 so I think you are ok From: "Gold, Andrea (NIH/NIMH) [F]"

[Freesurfer] gzip: stdin: unexpected end of file

After downloading CentOS 6 x86_64 (64b) stable v6.0.0 unzipping on Ubunt 16.04 (64b) machine with tar -C /usr/local -xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz Returns an error: gzip: stdin: unexpected end of file tar: Child returned status 1 tar: Error is not recoverable:

[Freesurfer] Re-running after Base Image Edits

Hi there, We are attempting edits on base images and a couple of questions came up when re-running through the pipeline: 1. After cp, wm, or pial edits on the base image, is it okay to simply start at ‘-autorecon2’ or must the specific starting points be used? (ie. “-autorecon2-cp”,

Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue

Glad to hear! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Abigail Waters [awate...@suffolk.edu] Sent: Tuesday, February 21, 2017 7:31 PM To: Freesurfer support list Subject: Re: [Freesurfer] -trac-all -prep

Re: [Freesurfer] Freeview

Thank you very much ,it was a great help . Best Regards, Nazanin On Tue, Feb 21, 2017 at 7:34 PM, Ruopeng Wang wrote: > Just open FreeSurferColorLUT.txt file in your freesurfer installation > directory, you should be able to figure the format. > > On Feb 21, 2017,

Re: [Freesurfer] cluster as ROI

I've attached it for you as a .txt file - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 21. Februar 2017 17:47:23 Betreff: Re: [Freesurfer] cluster as ROI Can you send the terminal output? On 02/21/2017

Re: [Freesurfer] “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"

Sorry for the delay. I could not replicate this error on my end. It looks like the $FREESURFER_HOME/subjects/fsaverage/label/lh.aparc.annot might be bad on your system. Try this tksurfer fsaverage lh inflated -aparc does that generate the same errors? On 02/16/2017 02:35 PM, Uquillas,

Re: [Freesurfer] cluster as ROI

Does this file exist? /nobackup/etsch2/kids/prepost-61kids//qdec/2016.12.08-40kids-2stagemodel/rh-area_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh On 02/21/2017 11:54 AM, Clara Kühn wrote: > I've attached it for you as a .txt file > > - Ursprüngliche Mail - >

[Freesurfer] contrast matrix for one-way ANOVA with 1 factor, 4 groups

Hi, I am trying to run a cortical thickness analysis comparing four groups – my goal is to conduct an omnibus F-test testing for any group differences. I have 0 covariates/nuisance regressors. This would be equivalent to the “Contrast 4 group.effect.mtx” in this page, for 3 groups:

Re: [Freesurfer] mri_glmfit-sim

On 02/21/2017 02:26 PM, Shane Schofield wrote: > Hi, > > I have 3 beginner questions about the use of mri_glmfit-sim > > 1. Under what type of circumstances should I run mri_glmfit-sim with > permutation simulations? This is a little bit of an open question as there is a big debate going on

[Freesurfer] Fwd: Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?

-- Forwarded message -- From: Kaiming Yin Date: 1 July 2016 at 11:15 Subject: Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ? To: FreeSurfer Mailing List Dear guys, Could I ask which value in

Re: [Freesurfer] -trac-all -prep FS 5.3 Memory Allocation Issue

Hi - So I went ahead an uninstalled and then reinstalled the update to see if that fixed the problem, and it seems to be working fine now. Thank you for your help! Best Abby From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on

Re: [Freesurfer] apply CVS morph to a list of coordinates

Hi Lilla, It’ s a Mac Pro with 64Gb Ram. Best, Cristian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to

Re: [Freesurfer] cluster as ROI

yes! - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 21. Februar 2017 17:58:37 Betreff: Re: [Freesurfer] cluster as ROI Does this file exist?

Re: [Freesurfer] cluster as ROI

then that is the "ocn" file to use with mri_segstats On 02/21/2017 12:18 PM, Clara Kühn wrote: > yes! > > - Ursprüngliche Mail - > Von: "Douglas N Greve" > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 21. Februar 2017 17:58:37 > Betreff: Re:

Re: [Freesurfer] cluster as ROI

ah! Perfect, thank you! I'll give that a try. - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 21. Februar 2017 18:23:48 Betreff: Re: [Freesurfer] cluster as ROI then that is the "ocn" file to use with

Re: [Freesurfer] cluster as ROI

I have one last question about the whole thing. What is the measurement in the output file? My subjects have values between 0.6 and 1.5. As the measure is surface area I was expecting different numbers. Do I have to multiply by some constant to get to mm²? Thank you Clara - Ursprüngliche

Re: [Freesurfer] cluster as ROI

That will be the average value over the vertices in the ROI, which is not what you want for surface area. Add --accumulate to the mri_segstats command line to get the total area On 02/21/2017 12:43 PM, Clara Kühn wrote: > I have one last question about the whole thing. > > What is the

Re: [Freesurfer] cluster as ROI

that doesn't change the values. I've attached the file for you. - Ursprüngliche Mail - Von: "Douglas N Greve" An: freesurfer@nmr.mgh.harvard.edu Gesendet: Dienstag, 21. Februar 2017 18:56:17 Betreff: Re: [Freesurfer] cluster as ROI That will be the average

Re: [Freesurfer] cluster as ROI

sorry, gave you the wrong flag. Use --sumwf instead of --accumulate On 02/21/2017 01:08 PM, Clara Kühn wrote: > that doesn't change the values. I've attached the file for you. > > - Ursprüngliche Mail - > Von: "Douglas N Greve" > An:

[Freesurfer] mri_glmfit-sim

Hi, I have 3 beginner questions about the use of mri_glmfit-sim 1. Under what type of circumstances should I run mri_glmfit-sim with permutation simulations?  2. The voxel threshold of 0.01 (cache 2) is used a lot. Is this too lenient in cortical thickness comparisons?  3. About the sign of

Re: [Freesurfer] Convolving external regressors with HRF

Hi Doug, Since our external regressors are stimulus-related (e.g. mean luminance of stimuli), we need to convolve them with a hemodynamic response function. In mkanalysis-sess, we have used -spmhrf 0 to model conditions. Is there a code or Matlab script for HRF convolution, so that we apply

Re: [Freesurfer] Convolving external regressors with HRF

You can use the following matlab code. You can ignore the warning printed after the toepliz operation. The OriginalRegressor should be a vector of length Ntp, then write out the NewRegressor to a new external regressor file. TR=2; % seconds Ntp=100; t = TR*[0:Ntp-1]'; h = fast_spmhrf(t); a

Re: [Freesurfer] contrast matrix for one-way ANOVA with 1 factor, 4 groups

That four group test will yield the same exact result as 1 -1 0 0 1 0 -1 0 1 0 0 -1 so I think you are ok On 02/21/2017 03:09 PM, Gold, Andrea (NIH/NIMH) [F] wrote: > > Hi, > > I am trying to run a cortical thickness analysis comparing four groups > – my goal is to conduct an omnibus F-test

Re: [Freesurfer] mri_normalize 5.4 vs v6

Hi Arman have you tried changing the windowing levels in whatever software you used to create that image? You can't get the exact same results in V6 as in V5.3 as the algorithm has changed a bit. cheers Bruce On Tue, 21 Feb 2017, Arman Eshaghi wrote: > Dear All, > > When I run

Re: [Freesurfer] cluster as ROI

You will have to run mri_glmfit-sim On 02/21/2017 04:07 AM, Clara Kühn wrote: > Hi Doug, > > I have a gamma.mgh file in glmdir/rh-Diff-1-3-Intercept-long.area-spc/ and I > also have a contrasts.sig.mgh file in the gmldir. > > Could either of these be used instead of csdbase.sig.ocn.mgh? Or how

[Freesurfer] Freeview X Error: BadValue

Hi FS gurus, I am remote logging in to nmr nexlin machines from my work iMAC and I am trying to view some freesurfer results with Freeview, but I am getting the following error: llebois@nexlin9:/eris/ressler/DD_FS_160222/150305_NTD015_FS/mri/assembly$ freeview -v nu.mgz

Re: [Freesurfer] -no-isrunning flag question

Hi Joe, you just want to make sure that no other process really is running otherwise they may conflict with each other e.g. by trying to write the same file at the same time. cheers Bruce On Tue, 21 Feb 2017, Joe Necus (PGR) wrote: Hello, As I understand, adding the -no-isrunning flag

Re: [Freesurfer] cluster as ROI

Can you send the terminal output? On 02/21/2017 11:44 AM, Clara Kühn wrote: > Hm. I already did that. In none of my glmdirs are files like the > csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran: > > mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir >

Re: [Freesurfer] cluster as ROI

Hm. I already did that. In none of my glmdirs are files like the csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran: mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir $SUBJECTS_DIR/average/multi-comp-cor/ --cache 3.0 abs --cwp 0.05 --2spaces Cheers Clara -

Re: [Freesurfer] “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"

Hi Doug, thanks so much for looking into this. I just ran that comman and I get the same errors indeed. Would you be able to recommend a way for us to fix this so we can look at the left hemi significant clusters after mri_glmfit-sim? Best, Fred On 2/21/17, 11:33 AM,

Re: [Freesurfer] Freeview

Just open FreeSurferColorLUT.txt file in your freesurfer installation directory, you should be able to figure the format. > On Feb 21, 2017, at 10:59 AM, N Saf wrote: > > Dear Ruopeng, > > Thank you for the fast response ,where can I learn how to create my custom > lookup

Re: [Freesurfer] Freeview

Dear Ruopeng, Thank you for the fast response ,where can I learn how to create my custom lookup table step by step ? and what the format of this file is?any help will be very appreciated. Best Regards, Nazanin On Tue, Feb 21, 2017 at 6:45 PM, Ruopeng Wang wrote: >

Re: [Freesurfer] “ERROR: Too many out-of-range vertex indices in MRISreadAnnotationIntoArray!"

I think your installation of FS got corrupted. Try downloading and reinstalling FS (same version of what you have). If you want, you can just copy over fsaverage from the new download. On 02/21/2017 11:50 AM, Uquillas, Federico D'Oleire wrote: > Hi Doug, thanks so much for looking into this. I

Re: [Freesurfer] Convolving external regressors with HRF

No, they are not On 02/17/2017 05:09 PM, Reza Rajimehr wrote: > During the functional analysis in FS-FAST, are the external regressors > convolved with the hemodynamic response function? > > Thanks, > Reza > > > ___ > Freesurfer mailing list >

[Freesurfer] cannot "git pull" from freeSurfer git repository

Dear experts, I am recently not able to pull from freeSurfer git repository. The error message is following: error: The requested URL returned error: 403 Forbidden (curl_result = 22, http_code = 403, sha1 = b3b71d49c42db73a6f1dad0229111dc3f900a1d3) error: Unable to find